NAME

       mapsembler - manual page for mapsembler 2.0.5+dfsg

DESCRIPTION

       NAME mapsembler, version 2.0.4 - Copyright INRIA - CeCILL License

       SYNOPSIS     ./maps/mapsembler     <starters.fasta>    <readsC1.fasta>    [<readsC2.fasta>
       [<readsC3.fasta] ...] [-E] [-t extension_type]  [-q  value]  [-k  value]  [-c  value]  [-d
       authorized_distance]  [-e  error_threshold] [-g value] [-i index_name] [-o name] [-m name]
       [-h]

       DESCRIPTION

              Mapsembler2 is a targeted assembly software. It takes as input a  set  of  NGS  raw
              reads  (fasta or fastq, gzipped or not) and a set of input sequences (starters). It
              first determines if each starter is read-coherent, e.g. whether reads  confirm  the
              presence  of  each  starter  in  the original sequence. Then for each read-coherent
              starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a
              graph, depending on the user choice.

       OPTIONS

       -E Extend only: avoid the mapping+substarter generation phase

       -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

       -q size_seed: will use seeds of length size_seed during the mapping process. Default:  25,
              value should be in [5-31]

       -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

       -d  authorized_distance:  a  substarter  is  distant  by   at   most   authorized_distance
              substitutions. Default: 2

       -e  error_threshold:  a nucleotide is corrected if occurs less than error_threshold times.
              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

       -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"

       -m file_name: write in file "file_name" the reads mapped on starters

       -h prints this message and exit

SEE ALSO

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

              info mapsembler

       should give you access to the complete manual.