Provided by: discosnp_1.0.1-3_amd64
kissnp2 - manual page for kissnp2 1.0.1
NAME kissnp, version 22.214.171.124 - Copyright INRIA - CeCILL License SYNOPSIS kissnp2/kissnp2 <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] -o name [-t] [-e length] [-l] [-b] [-k value] [-c value] [-g value] [-h] or: kissnp2/kissnp2 input_names_file.txt -o name [-t] [-e length] [-l] [-b] [-k value] [-c value] [-g value] [-h] with "input_names_file.txt" being a file containing on each line the name of read files DESCRIPTION "kissnp2", detects SNPs from read set(s). It should usually be followed by the "kissreads" for recovering coverage and quality information from reads. MANDATORY At least one read set. -o file_name_prefix: where to write outputs and debruijn graph structure files. OPTIONS -t extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with -T -T extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with -t -e length: extend found SNPs (option -t) and conserve only those whose min(left and right extension) is bigger or equal to "length" -l conserve low complexity SNPs. Default: false (filter out low complexity results) -b prints branching SNPs -k size_seed: will use seeds of length size_seed. Default: 27. -c min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2 -C max_coverage: a sequence is covered by at most max_coverage coherent reads. Default: infiny (=2147483647 on your computer :) ) -g estimated_genome_size: estimation of the size of the genome whose reads come from. It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion -h prints this message and exit This is kissnp2, version 126.96.36.199 The command line was: kissnp2/kissnp2 -h
The full documentation for kissnp2 is maintained as a Texinfo manual. If the info and kissnp2 programs are properly installed at your site, the command info kissnp2 should give you access to the complete manual.