FRCurve - Revision history

Gnarzisi: /* References */

2012-12-01T17:54:50Z

‎References

Gnarzisi at 17:52, 1 December 2012

2012-12-01T17:52:48Z

Floflooo: /* Documentation */

2011-05-23T07:03:06Z

‎Documentation

Floflooo: /* Documentation */

2011-05-23T06:31:28Z

‎Documentation

Gnarzisi at 13:36, 3 May 2011

2011-05-03T13:36:09Z

Gnarzisi: /* Overview */

2011-04-05T13:27:30Z

‎Overview

@@ Line 76: / Line 76: @@
 "Feature-by-Feature - Evaluating De Novo Sequence Assembly."
 '''PLoS ONE''' 7(2): e31002, February 2012. (DOI: 10.1371/journal.pone.0031002 [http://dx.plos.org/10.1371/journal.pone.0031002]).
 == Acknowledgements ==
 Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.

@@ Line 72: / Line 72: @@
 ''Comparing De Novo Genome Assembly: The Long and Short of It''.
 '''PLoS ONE''' 6(4):e19175. April 2011 (DOI: [http://dx.plos.org/10.1371/journal.pone.0019175 10.1371/journal.pone.0019175]).
 == Acknowledgements ==
 Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.

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 Following the AMOS philosophy, the FRCurve is implemented as a pipeline that consists of two steps:
 * 1. invocation to the amosvalidate tool to compute the features for the set of contigs;
-* 2. invocation to the FRC module
+* 2. invocation to the FRC module, getFRCvalues
 The name of the pipeline in the AMOS distribution is "FRCurve_pipeline".

@@ Line 27: / Line 27: @@
 Documentation on how to run FRCurve is obtained by typing:
-    FRCurve_pipeline -h
+    FRCurve -h
 The usage message is:
@@ Line 33: / Line 33: @@
   Feature-Response Curve pipeline
   Usage:
-       FRCurve_pipeline [params] \
+       FRCurve [params] \
                  -D GENOME_SIZE=<n>              - Genome size (number of bps)
                  -D BANK=<n>                     - AMOS bank name

@@ Line 69: / Line 69: @@
 == References ==
-Coming soon...
+Narzisi G. and Mishra B.:
 == Acknowledgements ==
 Research reported here was supported by grants from NSF CDI program and Abraxis BioScience, LLC.

@@ Line 3: / Line 3: @@
 == Overview ==
-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).
+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).
 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
@@ Line 10: / Line 10: @@
 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
 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.
 == Documentation ==