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

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

       should give you access to the complete manual.

kissnp2 1.2.6                                     November 2014                                       KISSNP2(1)