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.