NAME

       mapsembler_extend  - extends a DNA sequence of interest given a set of reads, by computing
       a targeted micro assembly

SYNOPSIS

       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

       Mapsembler  2  extends  a  DNA  sequence  of interest given a set of reads, by computing a
       targeted micro assembly.

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

AUTHOR

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