Minimus - Revision history

Floflooo: /* Publication */

2011-11-12T02:23:21Z

‎Publication

Decaos: /* Basic usage */

2010-11-09T19:57:57Z

‎Basic usage

Trgibbons: /* Overview */

2010-01-29T16:25:49Z

‎Overview

Trgibbons: /* Basic usage */

2010-01-14T22:28:16Z

‎Basic usage

Trgibbons: /* Basic usage */

2010-01-14T22:26:56Z

‎Basic usage

Trgibbons: /* Overview */

2010-01-14T22:17:46Z

‎Overview

@@ Line 51: / Line 51: @@
 [http://www.biomedcentral.com/1471-2105/8/64 Minimus: a fast, lightweight genome assembler]
-Sommer, DD, Delcher, AL, Salzberg, SL, and Pop, M. (2007) BMC Bioinformatics, 8:64doi:10.1186/1471-2105-8-64.
+Sommer, DD, Delcher, AL, Salzberg, SL, and Pop, M. (2007) BMC Bioinformatics, 8:64, doi:10.1186/1471-2105-8-64.
-−
-−
-−
 == Acknowledgements ==
 The development of minimus was supported by the National Institutes of Health under grants R01-LM06845 and R01-LM007938 to SLS and by Department of Homeland Security cooperative agreement W81XWH-05-2-0051.

@@ Line 37: / Line 37: @@
 The toAmos file conversion utility is the most general and probably the most useful of the file conversion utilities included with minimus. More information about toAmos and the [[File_conversion_utilities | other file conversion utilities]] can be found in the [[AMOS | AMOS documentation wiki]]. For example, you can include quality data from a Phred style quality score file by running [[ToAmos | toAmos]] with the -q option as follows:
-  toAmos -s my_reads.fasta -q my_reads.qual -o my_reads.afg
+  toAmos -s my_reads.fasta -q my_reads.qual -o asm_reads.afg
 Minimus can also be called with the following equivalent command:
-  runAmos -C $AMOSBASE/src/Pipeline/minimus.acf my_reads
+  runAmos -C $AMOSBASE/src/Pipeline/minimus.acf asm_reads
 The AMOS package also includes other helpful tools such as [[Hawkeye]], which is useful for evaluating your assembly with respect to paired-end reads. It can be run on the minimus bank with the following command:
-  hawkeye my_reads.bnk/
+  hawkeye asm_reads.bnk/
 == Publication ==

@@ Line 1: / Line 1: @@
 == Overview ==
-Minimus is an assembly pipeline designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding.
+Minimus is one of several assembly pipelines included in the AMOS software package. It is designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding.
 Minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules which share information through a central file bank:

@@ Line 30: / Line 30: @@
 To run minimus will you need a set of sequence files. Assuming you have a set of reads in fasta format called '''my_reads.seq''', you can run minimus with the following two commands:
-  `toAmos -s my_reads.seq -o my_reads.afg'
+  toAmos -s my_reads.seq -o my_reads.afg
-  `minimus my_reads'
+  minimus my_reads
 The output will be a fasta formatted file called '"my_reads.fasta"', a contig file with details about the assembly of each contig called '"my_reads.contig"', and an AMOS bank folder with various files used internally by minimus.
 The toAmos file conversion utility is the most general and probably the most useful of the file conversion utilities included with minimus. More information about toAmos and the [[File_conversion_utilities | other file conversion utilities]] can be found in the [[AMOS | AMOS documentation wiki]]. For example, you can include quality data from a Phred style quality score file by running [[ToAmos | toAmos]] with the -q option as follows:
-  `toAmos -s my_reads.fasta -q my_reads.qual -o my_reads.afg'
+  toAmos -s my_reads.fasta -q my_reads.qual -o my_reads.afg
 Minimus can also be called with the following equivalent command:
-  `runAmos -C $AMOSBASE/src/Pipeline/minimus.acf my_reads'
+  runAmos -C $AMOSBASE/src/Pipeline/minimus.acf my_reads
 The AMOS package also includes other helpful tools such as [[Hawkeye]], which is useful for evaluating your assembly with respect to paired-end reads. It can be run on the minimus bank with the following command:
-  `hawkeye my_reads.bnk/'
+  hawkeye my_reads.bnk/
 == Publication ==

@@ Line 30: / Line 30: @@
 To run minimus will you need a set of sequence files. Assuming you have a set of reads in fasta format called '''my_reads.seq''', you can run minimus with the following two commands:
-  toAmos -s my_reads.seq -o my_reads.afg
+  `toAmos -s my_reads.seq -o my_reads.afg'
-  minimus my_reads
+  `minimus my_reads'
 The output will be a fasta formatted file called '"my_reads.fasta"', a contig file with details about the assembly of each contig called '"my_reads.contig"', and an AMOS bank folder with various files used internally by minimus.
 The toAmos file conversion utility is the most general and probably the most useful of the file conversion utilities included with minimus. More information about toAmos and the [[File_conversion_utilities | other file conversion utilities]] can be found in the [[AMOS | AMOS documentation wiki]]. For example, you can include quality data from a Phred style quality score file by running [[ToAmos | toAmos]] with the -q option as follows:
-  toAmos -s my_reads.fasta -q my_reads.qual -o my_reads.afg
+  `toAmos -s my_reads.fasta -q my_reads.qual -o my_reads.afg'
 Minimus can also be called with the following equivalent command:
-  runAmos -C $AMOSBASE/src/Pipeline/minimus.acf my_reads
+  `runAmos -C $AMOSBASE/src/Pipeline/minimus.acf my_reads'
 The AMOS package also includes other helpful tools such as [[Hawkeye]], which is useful for evaluating your assembly with respect to paired-end reads. It can be run on the minimus bank with the following command:
-  hawkeye my_reads.bnk/
+  `hawkeye my_reads.bnk/'
 == Publication ==

@@ Line 1: / Line 1: @@
 == Overview ==
-minimus is an assembly pipeline designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding.
+Minimus is an assembly pipeline designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding.
-minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
+Minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules which share information through a central file bank:
-* [[hash-overlap]] - computes the overlaps between the reads using a modified version of the Smith-Waterman local alignment algorithm
+* [[hash-overlap]] - Computes the overlaps between the reads using a modified version of the Smith-Waterman local alignment algorithm
-* [[tigger]] - uses the read overlaps to generate the layouts of reads representing individual contigs
+* [[tigger]] - Uses the read overlaps to generate the layouts of reads representing individual contigs
-* [[make-consensus]] - refines the layouts produced by the tigger to generate accurate multiple alignments within the reads
+* [[make-consensus]] - Refines the layouts produced by the tigger to generate accurate multiple alignments within the reads
-minimus uses as AMOS messages as both the inputs and the outputs. Please see the [[File conversion utilities]] documentation for more information.
+Minimus uses AMOS message files as both the inputs and the outputs. Please see the [[File conversion utilities]] documentation for more information.
-[[minimus2]] is a modified version of the minimus pipeline designed for merging two sequence sets. Instead of hash-overlap it uses a nucmer based overlap detector which is much faster.
+[[minimus2 | Minimus2]] is a modified version of the minimus pipeline designed for merging two sequence sets. Instead of hash-overlap it uses a nucmer based overlap detector which is much faster.
-−
 == Documentation ==