table of contents
| KISSNP2(1) | User Commands | KISSNP2(1) |
NAME¶
kissnp2 - manual page for kissnp2 1.2.5DESCRIPTION¶
NAME kissnp, version DiscoSnp - kissnp submodule 1.2.5 - 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:
- with "input_names_file.txt" being a file containing on each line the name of read files
- "kissnp2", detects SNPs from read set(s). It should usually be followed by the "kissreads" for recovering coverage and quality information from reads.
- At least one read set. -o file_name_prefix: where to write outputs and debruijn graph structure files.
-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 1.2.5 - Copyright INRIA - CeCILL License The command
line was: kissnp2/kissnp2 -h
SEE ALSO¶
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
| October 2014 | kissnp2 1.2.5 |