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contributors:team_4_page [2015/05/08 02:05] JaredC |
contributors:team_4_page [2015/05/08 02:52] JaredC |
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% ./autogen.sh | % ./autogen.sh | ||
% ./configure --prefix=/campusdata/BME235\ | % ./configure --prefix=/campusdata/BME235\ | ||
+ | % --enable-maxk=96\ #must be a multiple of 32 | ||
% --enable-dependency-tracking\ | % --enable-dependency-tracking\ | ||
% --with-boost=/campusdata/BME235/include/boost\ | % --with-boost=/campusdata/BME235/include/boost\ | ||
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=====ABySS parameters===== | =====ABySS parameters===== | ||
- | Parameters of the driver script, abyss-pe | + | Parameters of the driver script, abyss-pe, and their [default value] |
* a: maximum number of branches of a bubble [2] | * a: maximum number of branches of a bubble [2] | ||
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* E: minimum erosion k-mer coverage per strand [1] | * E: minimum erosion k-mer coverage per strand [1] | ||
* j: number of threads [2] | * j: number of threads [2] | ||
- | * k: size of k-mer (bp) | + | * k: size of k-mer (bp) [no default] |
* l: minimum alignment length of a read (bp) [k] | * l: minimum alignment length of a read (bp) [k] | ||
* m: minimum overlap of two unitigs (bp) [30] | * m: minimum overlap of two unitigs (bp) [30] | ||
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Above command will report all abyss-pe parameters that are set from various origins. However it will not operate ABySS programs. | Above command will report all abyss-pe parameters that are set from various origins. However it will not operate ABySS programs. | ||
- | =====ABySS Programs===== | + | =====Running ABySS===== |
abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are: | abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are: | ||
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Print the commands that would be executed, but do not execute them. | Print the commands that would be executed, but do not execute them. | ||
+ | ===Commands of abyss-pe=== | ||
+ | * default: Equivalent to `scaffolds scaffolds-dot stats'. | ||
+ | * unitigs: Assemble unitigs. | ||
+ | * unitigs-dot: Output the unitig overlap graph. | ||
+ | * pe-sam: Map paired-end reads to the unitigs and output a SAM file. | ||
+ | * pe-bam: Map paired-end reads to the unitigs and output a BAM file. | ||
+ | * pe-index: Generate an index of the unitigs used by abyss-map. | ||
+ | * contigs: Assemble contigs. | ||
+ | * contigs-dot: Output the contig overlap graph. | ||
+ | * mp-sam: Map mate-pair reads to the contigs and output a SAM file. | ||
+ | * mp-bam: Map mate-pair reads to the contigs and output a BAM file. | ||
+ | * mp-index: Generate an index of the contigs used by abyss-map. | ||
+ | * scaffolds: Assemble scaffolds. | ||
+ | * scaffolds-dot: Output the scaffold overlap graph. | ||
+ | * stats: Display assembly contiguity statistics. | ||
+ | * clean: Remove intermediate files. | ||
+ | * version: Display the version of abyss-pe. | ||
+ | * versions: Display the versions of all programs used by abyss-pe. | ||
+ | * help: Display a helpful message. | ||
+ | |||
+ | ===Programs in pipeline=== | ||
abyss-pe uses the following programs, which must be found in your PATH: | abyss-pe uses the following programs, which must be found in your PATH: | ||
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* abyss-filtergraph: remove shim contigs from the overlap graph | * abyss-filtergraph: remove shim contigs from the overlap graph | ||
* abyss-fixmate: fill the paired-end fields of SAM alignments | * abyss-fixmate: fill the paired-end fields of SAM alignments | ||
- | * abyss-map: map reads to a reference sequence | + | * abyss-map: map reads to a reference sequence (BW transform) |
* abyss-scaffold: scaffold contigs using distance estimates | * abyss-scaffold: scaffold contigs using distance estimates | ||
* abyss-todot: convert graph formats and merge graphs | * abyss-todot: convert graph formats and merge graphs | ||
+ | New to Version 1.3.5 (Mar 05, 2013) | ||
+ | * abyss-mergepairs: Merges overlapping read pairs. | ||
+ | * abyss-layout: Layout contigs using the sequence overlap graph. | ||
+ | * abyss-samtobreak: Calculate contig and scaffold contiguity and correctness metrics. | ||
+ | New to Version 1.5.2 (Jul 10, 2014) | ||
+ | * konnector: fill the gaps between paired-end reads by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph | ||
+ | * abyss-bloom: construct reusable bloom filter files for input to Konnector | ||
=====ABySS pipeline===== | =====ABySS pipeline===== |