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crass-assembler(1) |
General Commands Manual |
crass-assembler(1) |
NAME
crass-assembler — An assembly wrapper for crass
SYNOPSIS
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crass-assembler |
-x crass.crispr -s CONTIGS -i INPUT_DIR -g GROUP [-ohV] [--velvet | --cap3] |
DESCRIPTION
crass-assembler is a wrapper for a couple of genome assembly algorithms that can be used to reconstruct CRISPR loci.
crass-assembler is an add-on to
crass(1) that produces an ordering of spacers from a CRISPR loci.
crass-assembler processes this information and passes the reads from individual CRISPR strains onto one of the genome assemblers for generation of contigs.
OPTIONS
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crass-assembler [-hV] [-o PATH] -i PATH -g INT -x PATH -s INT[,INT] [--velvet | --cap3]
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-g INT --group INT
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The group number of the CRISPR that you want to assemble
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-h --help
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Output basic usage informtion to screen
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-i PATH --inDir PATH
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The name of the input directory
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-o PATH --outDir PATH
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The name of the output directory [Default: inDir]
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-s INT[,INT] --segments INT[,INT]
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A comma separated list of numbered segments to assemble from the specified group
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-V --version
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Print version and copy right information
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-x FILE --xml FILE
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The .crispr xml output file created by crass
DIAGNOSTICS
The crass-assembler utility exits 0 on success, and >0 if an error occurs.