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