NAME

       kissreads2 - enhances the kissnp2 results by computing per read set

DESCRIPTION

       [Kissreads2 options]

       -x     (0 arg) :    radseq option, homogeneous read depth along the prediction

       -predictions
              (1 arg) :    Input predictions

       -reads (1 arg) :    Input reads

       -unco  (1 arg) :    Output uncoherent file name  [default '/dev/null']

       -co    (1 arg) :    Output coherent file name

       -hamming
              (1 arg) :    Maximal hamming distance authorized while maping  [default '1']

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

       -k     (1 arg) :    Size of k, used as minial overlap and kmer spanning read coherence  [default '31']

       -index_stride
              (1 arg) :    Index Stride  [default '2']

       -size_seeds
              (1 arg) :    Size of the used seeds (distinct from the size of k)  [default '25']

       -output_fasta
              (0 arg) :    Output standard Fasta.  By  default  the  output  is  formatted  especially  for  the
              discoSnp++ pipeline

       -genotype
              (0 arg) :    Compute genotypes

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

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

       -version
              (0 arg) :    version

       -help  (0 arg) :    help

AUTHOR

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

kissreads2 2.3.0                                  January 2019                                     KISSREADS2(1)