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contributors:team_4_page [2015/05/08 02:19] JaredC |
contributors:team_4_page [2015/05/08 02:25] JaredC [ABySS Programs] |
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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: | ||