mapsembler_extend(1) manual page for mapsembler_extend 2.2.3+dfsg


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]




-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