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MAPSEMBLER_EXTEND

NAME

mapsembler_extend − manual page for mapsembler_extend 2.2.3+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.

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