kissnp2 - detects SNPs and indels from read sets

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

kissnp2 2.3.0                                     January 2019                                        KISSNP2(1)

       [Kissnp2 options]

       -x     (0 arg) :    keep truncated bubbles, that have no successors on the 2 paths at the same position

       -P     (1 arg) :    maximal number of polymorphism per bubble  [default '1']

       -D     (1 arg) :    maximal size of a predicted indel  [default '0']

       -dont_output_first_coverage (0 arg) :
              Don't  output  the  first coverage threshold. Use this option whent the reference file is used for
              finding the variants

       -in    (1 arg) :    input file (likely a hdf5 file)

       -coverage_file
              (1 arg) :    File (.h5) generated by kissnp2, containing  the  coverage  threshold  per  read  set
              [default '_removemeplease']

       -out   (1 arg) :    output name

       -T     (0  arg)  :     extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible
              with -t-t     (0 arg) :    extend  found  and  stop  at  first  polymorphism  (strict  extension=unitigs)  SNPs.
              Uncompatible with -T-max_symmetrical_crossroads (1 arg) :
              In  b2  mode  only:  maximal  number  of  symmetrical croasroads traversed while trying to close a
              bubble. Default: no limit  [default '-1']

       -b     (1 arg) :    branching mode

              0: forbid SNPs for which any of the two paths is branching (high precision, low recall) 1:  forbid
              SNPs for which the two paths are branching (e.g. the two paths can be created either with a 'A' or
              a  'C'  at  the  same  position (default value) 2: No limitation on branching (low precision, high
              recall)  [default '1']

       -max_ambigous_indel
              (1 arg) :    Maximal size of ambiguity of INDELs. INDELS whose ambiguity is higher than this value
              are not output  [default '20']

       -l     (0 arg) :    conserve low complexity SNPs

       -nb-cores
              (1 arg) :    number of cores  [default '0']

       -verbose
              (1 arg) :    verbosity level  [default '1']

       -version
              (0 arg) :    version

       -help  (0 arg) :    help

       -bfs-max-depth
              (1 arg) :    maximum depth for BFS  [default '200']

       -bfs-max-breadth
              (1 arg) :    maximum breadth for BFS  [default '20']

       kissnp2 - detects SNPs and indels from read sets