crass-assembler(1) General Commands Manual crass-assembler(1)


crass-assemblerAn assembly wrapper for crass


crass-assembler -x crass.crispr -s CONTIGS -i INPUT_DIR -g GROUP [-ohV] [--velvet | --cap3]


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.


crass-assembler [-hV] [-o PATH] -i PATH -g INT -x PATH -s INT[,INT] [--velvet | --cap3]
-g INT --group INT
The group number of the CRISPR that you want to assemble
-h --help
Output basic usage informtion to screen
-i PATH --inDir PATH
The name of the input directory
-o PATH --outDir PATH
The name of the output directory [Default: inDir]
-s INT[,INT] --segments INT[,INT]
A comma separated list of numbered segments to assemble from the specified group
-V --version
Print version and copy right information
-x FILE --xml FILE
The .crispr xml output file created by crass


The crass-assembler utility exits 0 on success, and >0 if an error occurs.


crass(1), crisprtools(1)
17/04/13 Darwin