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.