NAME

       mapsembler2_extremities - performs the first step of Mapsembler2_extend

SYNOPSIS

       mapsembler2_extremities  --k  <kmersize>  --starters  <fasta> --reads <dataset> --output <substarterfile>
       [optional arguments]

DESCRIPTION

       This modules performs the first step of Mapsembler2_extend. For  each  starter,  it  outputs  a  list  of
       extremities of the starter (of length *k*) are found in the reads, up to 1 indel or mismatch.

OPTIONS

       --k (1 arg):
              kmer size that will be used for mapsembler2  [default '']

       --starters (1 arg):
              starters fasta file  [default '']

       --reads(1 arg):
              reads  dataset file name. Several reads sets can be provided, surrounded by "'s and separated by a
              space (e.g. --reads "reads1.fa reads2.fa")  [default '']

       --output (1 arg):
              output substarters file name  [default '']

       --min-solid-subkmer (1 arg):
              minimim abundance to keep a subkmer  [default '3']

       -debug (0 arg):
              debugging

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

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

       -help (0 arg):
              display help about possible options

AUTHOR

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

mapsembler2_extremities 2.2.4                     October 2018                        MAPSEMBLER2_EXTREMITIES(1)