http://amos.sourceforge.net/wiki/api.php?action=feedcontributions&feedformat=atom&user=GnarzisiAMOS WIKI - User contributions [en]2026-04-30T18:03:03ZUser contributionsMediaWiki 1.23.5http://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2012-12-01T17:54:50Z<p>Gnarzisi: /* References */</p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve (FRC) characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
FRC's properties:<br />
<ul><br />
<li>The FRC can be used as a metric to compare the assembly quality of multiple assemblers.</li><br />
<li>The FRC does not require any reference sequence (except an estimate of the genome size) to be used for validation, thus making it a very useful tool in de novo sequencing projects. </li><br />
<li>Separate FRCs can be generated for each feature type enabling to scrutinize the relative strengths and weaknesses of different assemblers.</li><br />
</ul><br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module, getFRCvalues<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve is obtained by typing:<br />
<br />
FRCurve -h<br />
<br />
The usage message is:<br />
<br />
Feature-Response Curve pipeline<br />
Usage: <br />
FRCurve [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
<br />
Description:<br />
The Feature-Response curve characterizes the sensitivity (coverage) <br />
of the sequence assembler as a function of its discrimination threshold (number of features).<br />
Given any set of features compute by the amosvalidate pipeline, the response (quality) <br />
of the assembler output is analyzed as a function of the maximum number of possible <br />
errors (features) allowed in the contigs. <br />
For more details see the wiki page at: <br />
http://sourceforge.net/apps/mediawiki/amos/index.php?title=FRCurve<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
Output file format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = cumulative size of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Narzisi G. and Mishra B.:<br />
''Comparing De Novo Genome Assembly: The Long and Short of It''.<br />
'''PLoS ONE''' 6(4):e19175. April 2011 (DOI: [http://dx.plos.org/10.1371/journal.pone.0019175 10.1371/journal.pone.0019175]).<br />
<br />
Vezzi F., Narzisi G., and Mishra B.:<br />
"Feature-by-Feature - Evaluating De Novo Sequence Assembly." <br />
'''PLoS ONE''' 7(2): e31002, February 2012. (DOI: 10.1371/journal.pone.0031002 [http://dx.plos.org/10.1371/journal.pone.0031002]).<br />
<br />
Schatz M. C., Phillippy A. M., Sommer D., Delcher A. L., Puiu D., Narzisi G., Salzberg S. L., Pop M.:<br />
"Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies."<br />
'''Briefings in Bioinformatics''', December 2011. (DOI: 10.1093/bib/bbr074 [http://bib.oxfordjournals.org/content/early/2011/12/23/bib.bbr074.full]).<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2012-12-01T17:52:48Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve (FRC) characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
FRC's properties:<br />
<ul><br />
<li>The FRC can be used as a metric to compare the assembly quality of multiple assemblers.</li><br />
<li>The FRC does not require any reference sequence (except an estimate of the genome size) to be used for validation, thus making it a very useful tool in de novo sequencing projects. </li><br />
<li>Separate FRCs can be generated for each feature type enabling to scrutinize the relative strengths and weaknesses of different assemblers.</li><br />
</ul><br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module, getFRCvalues<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve is obtained by typing:<br />
<br />
FRCurve -h<br />
<br />
The usage message is:<br />
<br />
Feature-Response Curve pipeline<br />
Usage: <br />
FRCurve [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
<br />
Description:<br />
The Feature-Response curve characterizes the sensitivity (coverage) <br />
of the sequence assembler as a function of its discrimination threshold (number of features).<br />
Given any set of features compute by the amosvalidate pipeline, the response (quality) <br />
of the assembler output is analyzed as a function of the maximum number of possible <br />
errors (features) allowed in the contigs. <br />
For more details see the wiki page at: <br />
http://sourceforge.net/apps/mediawiki/amos/index.php?title=FRCurve<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
Output file format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = cumulative size of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Narzisi G. and Mishra B.:<br />
''Comparing De Novo Genome Assembly: The Long and Short of It''.<br />
'''PLoS ONE''' 6(4):e19175. April 2011 (DOI: [http://dx.plos.org/10.1371/journal.pone.0019175 10.1371/journal.pone.0019175]).<br />
<br />
Vezzi F., Narzisi G., and Mishra B.:<br />
"Feature-by-Feature - Evaluating De Novo Sequence Assembly." <br />
'''PLoS ONE''' 7(2): e31002, February 2012. (DOI: 10.1371/journal.pone.0031002 [http://dx.plos.org/10.1371/journal.pone.0031002]).<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-05-03T13:36:09Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve (FRC) characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
FRC's properties:<br />
<ul><br />
<li>The FRC can be used as a metric to compare the assembly quality of multiple assemblers.</li><br />
<li>The FRC does not require any reference sequence (except an estimate of the genome size) to be used for validation, thus making it a very useful tool in de novo sequencing projects. </li><br />
<li>Separate FRCs can be generated for each feature type enabling to scrutinize the relative strengths and weaknesses of different assemblers.</li><br />
</ul><br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Feature-Response Curve pipeline<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
<br />
Description:<br />
The Feature-Response curve characterizes the sensitivity (coverage) <br />
of the sequence assembler as a function of its discrimination threshold (number of features).<br />
Given any set of features compute by the amosvalidate pipeline, the response (quality) <br />
of the assembler output is analyzed as a function of the maximum number of possible <br />
errors (features) allowed in the contigs. <br />
For more details see the wiki page at: <br />
http://sourceforge.net/apps/mediawiki/amos/index.php?title=FRCurve<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
Output file format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = cumulative size of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Narzisi G. and Mishra B.:<br />
''Comparing De Novo Genome Assembly: The Long and Short of It''.<br />
'''PLoS ONE''' 6(4):e19175. April 2011 (DOI: [http://dx.plos.org/10.1371/journal.pone.0019175 10.1371/journal.pone.0019175]).<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-04-05T13:27:30Z<p>Gnarzisi: /* Overview */</p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve (FRC) characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
FRC's properties:<br />
<ul><br />
<li>The FRC can be used as a metric to compare the assembly quality of multiple assemblers.</li><br />
<li>The FRC does not require any reference sequence (except an estimate of the genome size) to be used for validation, thus making it a very useful tool in de novo sequencing projects. </li><br />
<li>Separate FRCs can be generated for each feature type enabling to scrutinize the relative strengths and weaknesses of different assemblers.</li><br />
</ul><br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Feature-Response Curve pipeline<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
<br />
Description:<br />
The Feature-Response curve characterizes the sensitivity (coverage) <br />
of the sequence assembler as a function of its discrimination threshold (number of features).<br />
Given any set of features compute by the amosvalidate pipeline, the response (quality) <br />
of the assembler output is analyzed as a function of the maximum number of possible <br />
errors (features) allowed in the contigs. <br />
For more details see the wiki page at: <br />
http://sourceforge.net/apps/mediawiki/amos/index.php?title=FRCurve<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
Output file format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = cumulative size of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-03-28T18:32:59Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Feature-Response Curve pipeline<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
<br />
Description:<br />
The Feature-Response curve characterizes the sensitivity (coverage) <br />
of the sequence assembler as a function of its discrimination threshold (number of features).<br />
Given any set of features compute by the amosvalidate pipeline, the response (quality) <br />
of the assembler output is analyzed as a function of the maximum number of possible <br />
errors (features) allowed in the contigs. <br />
For more details see the wiki page at: <br />
http://sourceforge.net/apps/mediawiki/amos/index.php?title=FRCurve<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
Output file format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = cumulative size of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/AMOSAMOS2011-02-15T21:18:14Z<p>Gnarzisi: /* Validation and Visualization */</p>
<hr />
<div>{| align="right"<br />
| __TOC__<br />
|}<br />
<br />
The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler. Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.<br />
<br />
<br />
Quick links:<br />
* [[AMOS Getting Started]]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=134326 Download]<br />
* [http://sourceforge.net/projects/amos SourceForge project page]<br />
<br />
<br />
== Announcements ==<br />
<br />
* December 7th, 2010 - Version 3.0.0 of AMOS released!<br />
<br />
== Documentation ==<br />
Additional documentation in development through the [[AMOS Documentation Project]]<br />
<br />
<br />
=== Assemblers ===<br />
* [[ABBA]] - Assembly Boosted By Amino Acid Sequences<br />
* [[AMOScmp]] - comparative assembler<br />
* [[AMOScmp-shortReads]] - comparative assembler for short reads (Solexa,454)<br />
* [[AMOScmp-shortReads-alignmentTrimmed]] - comparative assembler for short reads that uses alignment based trimming<br />
* [[minimus]] - basic genome assembler for small datasets<br />
* [[minimus2]] - basic genome assembler for two datasets; can also be used as an assembly merge pipeline<br />
* [[Minimo]] - the minimus assembler with many more options<br />
<br />
=== Validation and Visualization ===<br />
* [[Hawkeye]] - assembly viewer<br />
* [[amosvalidate]] - assembly forensics<br />
* [[FRCurve]] - Feature-Response Curve<br />
* [[Benchmark]] - assembly benchmark data<br />
<br />
=== Scaffolding ===<br />
* [[Bambus]] - Open source standalone hierarchical scaffolding<br />
* [[Bambus2]] - Scaffolding Polymorphic Genomes and Metagenomes<br />
<br />
=== Trimming, Overlapping, & Error Correction ===<br />
* [[Figaro]] - statistical vector trimmer<br />
* [[UMD Overlapper]] - High quality overlap computations<br />
* [[KI Overlapper]] - Repeat aware overlapper<br />
* [[AutoEditor]] - Automatic correction of genome sequencing errors<br />
* [[FastqQC]] - Read composition and quality<br />
<br />
=== Utilities ===<br />
* [[File conversion utilities]] - converting data to and from AMOS<br />
* [[AMOS Utilities | AMOS Utilities]] - general utilities<br />
* [[runAmos]] - Pipeline executor<br />
<br />
=== AMOS Development ===<br />
* [[Programmer's guide]] - Getting started with the Source code<br />
* [[Infrastructure]] - Developer level details<br />
* [[Wiki guide]] - Guide for editing the wiki<br />
<br />
=== Assembly Tutorials ===<br />
* [http://www.cbcb.umd.edu/research/assembly_primer.shtml Assembly primer] - overview of genome assembly.<br />
* [http://www.cbcb.umd.edu/research/contig_representation.shtml Representing assemblies (not just in AMOS)]<br />
* [http://wgs-assembler.sourceforge.net Running Celera Assembler]<br />
<br />
<br />
<br />
== Download == <br />
The AMOS source if freely available for download from the File Release Section of our SourceForge project page. Please refer to the COPYING license included in the package for a description of the Artistic License, the same OSI certified open source license used by Perl and countless other packages. Not all of the above packages are included with the standard AMOS distribution, please see the homepage for the software you wish to download to verify that it is included with the AMOS source distribution.<br />
<br />
[http://sourceforge.net/project/showfiles.php?group_id=134326 Download from SourceForge]<br />
<br />
<br />
== Consortium members ==<br />
<br />
There have been numerous positive responses regarding the AMOS initiative, and we expect the list of involved organizations to grow significantly as the project matures. Please contact us if you want to join. The groups currently involved with the development of AMOS are listed below, along with their responsibilities and areas of expertise.<br />
<br />
* University of Maryland, Center for Bioinformatics and Computational Biology<br />
** project organization and direction<br />
** infrastructure<br />
** consensus<br />
** automated sequence editing<br />
** scaffolding<br />
** overlap detection<br />
** contig construction<br />
<br />
* The Institute for Genomic Research<br />
** production pipelines<br />
** automated finishing tools<br />
** error correction<br />
<br />
* Karolinska Institutet<br />
** overlap detection<br />
** error correction<br />
<br />
* Marine Biological Laboratory - Woods Hole<br />
** graphical interface<br />
** integration of assembly data with analysis (gene, polymorphism, etc.) information<br />
<br />
<br />
== Join the consortium ==<br />
<br />
All interested parties are welcome to join or aid the AMOS consortium. Please address all correspondence via Email to:<br />
<br />
amos-help (at) lists (dot) sourceforge (dot) net<br />
<br />
To receive information regarding new releases and developments, please subscribe to our moderated, low-traffic users' mailing list:<br />
<br />
amos-users (at) lists (dot) sourceforge (dot) net<br />
<br />
<br />
== Bug reports and support ==<br />
<br />
For AMOS bug reports or support requests, please browse our SourceForge project page or Email us at:<br />
<br />
amos-help (at) lists (dot) sourceforge (dot) net<br />
<br />
<br />
<br />
== Acknowledgements ==<br />
<br />
The AMOS consortium would like to thank the following organizations for their funding and/or support:<br />
* The National Institutes of Health - grants R01-LM06845, N01-AI-15447<br />
* The National Science Foundation - grants IIS-9902923, IIS-9820497<br />
* Department of Homeland Security - cooperative agreement W81XWH-05-2-0051<br />
* SourceForge.net</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T17:02:31Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding approximate genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T17:01:31Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus minimus] assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Benchmark here].<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T16:59:18Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
The figure below shows the Feature-Response Curve generated for the minimus assembly pipeline on the ''Brucella suis'' genome using the benchmark dataset available here.<br />
<br />
[[File:minimus_frc.jpeg|600px]]<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T16:53:55Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
[[File:minimus_frc.jpeg]]<br />
<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/File:Minimus_frc.jpegFile:Minimus frc.jpeg2011-02-15T16:52:02Z<p>Gnarzisi: Minimus Feature-Response Curve for Brucella suis</p>
<hr />
<div>Minimus Feature-Response Curve for Brucella suis</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T16:50:18Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== Example ==<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:38:04Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [http://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:30:27Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== People ==<br />
<br />
* [http://cims.nyu.edu/~gn387/ Giuseppe Narzisi] (PhD Student, NYU)<br />
* [http://www.cs.nyu.edu/mishra/ Bud Mishra] (Faculty, NYU)<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:26:51Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== References ==<br />
<br />
Coming soon...<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:25:41Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:24:24Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:23:31Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage: <br />
FRCurve_pipeline [params] \<br />
-D GENOME_SIZE=<n> - Genome size (number of bps)<br />
-D BANK=<n> - AMOS bank name<br />
<br />
Output:<br />
The Feature-Response curve (FRC) is saved in file "FRC.txt", while <br />
FRCs for each feature type are saved respectively in: <br />
"FRC_coverage.txt", "FRC_polymorphism.txt", "FRC_breakpoint.txt", <br />
"FRC_kmer.txt", "FRC_matepair.txt" and "FRC_misassembly.txt"<br />
File format:<br />
Each file contains the FRCs in 3-columns format<br />
- column 1 = feature threshold T;<br />
- column 2 = contigs' N50 associated to the threshold T in column 1;<br />
- column 3 = approximate coverage of the contigs whose number of features is <= T;<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:21:57Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
Documentation on how to run FRCurve_pipeline is obtained by typing:<br />
<br />
FRCurve_pipeline -h<br />
<br />
The usage message is:<br />
<br />
Usage:<br />
Minimo FASTA_IN [options]<br />
Options:<br />
-D QUAL_IN=<file> Input quality score file<br />
-D GOOD_QUAL=<n> Quality score to set for bases within the clear<br />
range if no quality file was given (default: 30)<br />
-D BAD_QUAL=<n> Quality score to set for bases outside clear range<br />
if no quality file was given (default: 10). If your<br />
sequences are trimmed, try the same value as GOOD_QUAL.<br />
-D MIN_LEN=<n> Minimum contig overlap length (at least 20 bp,<br />
default: 35)<br />
-D MIN_IDENT=<d> Minimum contig overlap identity percentage (between 0<br />
and 100 %, default: 98)<br />
-D ALN_WIGGLE=<d> Alignment wiggle value (from 2 for short reads to 15 for<br />
long reads, default: 2)<br />
-D FASTA_EXP=<n> Export results in FASTA format (0:no 1:yes, default: 0)<br />
-D ACE_EXP=<n> Export results in ACE format (0:no 1:yes, default: 0)<br />
-D OUT_PREFIX=< s> Prefix to use for the output file path and name<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:19:57Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:18:52Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
* 1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
* 2. invocation to the FRC module<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:17:34Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
1. invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
2. invocation to the FRC module<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:15:28Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps: <br />
1) invocation to the amosvalidate tool to compute the features for the set of contigs; <br />
2) invocation to the FRC module<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:13:03Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:12:35Z<p>Gnarzisi: </p>
<hr />
<div>'''FRCurve''': Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
Inspired by the standard receiver operating characteristic (ROC) curve, the Feature-Response curve characterizes the sensitivity (coverage) of the sequence assembler as a function of its discrimination threshold (number of features). <br />
<br />
The AMOS package provides an automated assembly validation pipeline called [https://sourceforge.net/apps/mediawiki/amos/index.php?title=Amosvalidate amosvalidate] that analyzes the output of an assembler using a variety of assembly quality metrics (or features). Examples of features include: (M) mate-pair orientations and separations, (K) repeat content by k-mer analysis, (C) depth-of-coverage, (P) correlated polymorphism in the read alignments, and (B) read alignment breakpoints to identify structurally suspicious regions of the assembly. After running amosvalidate on the output of the assembler, each contig is assigned a number of features that<br />
correspond to doubtful regions of the sequence.<br />
<br />
Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. More specifically, for a fixed feature<br />
threshold <math>\phi</math>�, the contigs are sorted by size and, starting from the longest, only those contigs are tallied, if their sum of features is <math>\leq \phi</math>��. For this set of contigs, the corresponding genome coverage is computed, leading to a single point of the Feature-Response curve.<br />
<br />
== Documentation ==<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:07:00Z<p>Gnarzisi: </p>
<hr />
<div>FRCurve: Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
== Documentation ==<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==<br />
<br />
Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.</div>Gnarzisihttp://amos.sourceforge.net/wiki/index.php/FRCurveFRCurve2011-02-15T02:05:22Z<p>Gnarzisi: Created page with 'FRCurve: Feature-Response Curve == Overview == == Documentation == == References == == Acknowledgements =='</p>
<hr />
<div>FRCurve: Feature-Response Curve<br />
<br />
== Overview ==<br />
<br />
== Documentation ==<br />
<br />
== References ==<br />
<br />
== Acknowledgements ==</div>Gnarzisi