contributors:team_4_page
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contributors:team_4_page [2015/05/08 02:16] JaredC |
contributors:team_4_page [2015/05/08 02:52] JaredC |
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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] | ||
| Line 74: | Line 74: | ||
| 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: | ||
| Line 102: | Line 123: | ||
| * 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===== | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
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