This is the command kissnp2 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
kissnp2 - manual page for kissnp2 1.2.6
DESCRIPTION
NAME kissnp, version DiscoSnp - kissnp submodule 1.2.6 - 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 INT:
0: forbid SNPs for wich any of the two paths is branching (high precision, low recall).
Default value
1: forbid SNPs for wich the two paths are branching (e.g. the two paths can be
created either with a 'A' or a 'C' at the same position 2: No limitation on
branching (low precision, high recall)
-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
DiscoSnp - kissnp submodule 1.2.6 - Copyright INRIA - CeCILL License The command line was:
kissnp2/kissnp2 -h
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