NAME

       mapsembler_extend - manual page for mapsembler_extend 2.2.4+dfsg

DESCRIPTION

       NAME mapsembler_extend, version 1.0.0 - Copyright INRIA - CeCILL License

       SYNOPSIS   ./mapsembler2_extend/mapsembler_extend   <extrem_kmers.fasta>   <readsC1.fasta>
       [<readsC2.fasta> [<readsC3.fasta] ...] [-t  extension_type]  [-k  value]  [-c  value]  [-g
       value] [-i index_name] [-o name] [-h]

       DESCRIPTION

              TODO

       OPTIONS

       -t extension_type. Default: 1

              1:  a  strict  sequence: any branching stops the extension 2: a consensus sequence:
              contiging approach 3: a strict graph: any branching is conserved in the graph 4:  a
              consensus  graph:  "small"  polymorphism  is  merged,  but  "large"  structures are
              represented

       -k size_kmers: Size of the k-mers used duriung the extension phase Default:  31.  Accepted
              range, depends on the compilation (make k=42 for instance)

       -c min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2

       -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

       -x node_len: limit max of nodes length. Default: 40

       -y graph_max_depth: limit max of graph depth.Default: 10000

       -i index_name: stores the index files in files starting with  this  prefix  name.  Can  be
              re-used latter. Default: "index"

              IF THE FILE "index_name.bloom" EXISTS: the index is not re-created

       -o file_name_prefix: where to write outputs. Default: "res_mapsembler"

       -p search_mod: kind of prosses Breadth or Depth. Default: Breadth

       -h prints this message and exit

SEE ALSO

       The  full  documentation  for mapsembler_extend is maintained as a Texinfo manual.  If the
       info and mapsembler_extend programs are properly installed at your site, the command

              info mapsembler_extend

       should give you access to the complete manual.