DESCRIPTION
NAME ./kissreads_graph/mapsembler2_kissreads_graph, version 1.0.0 Beta - Copyright INRIA - CeCILL License- -h prints this message and exit
DESCRIPTION ./kissreads_graph/mapsembler2_kissreads_graph maps the provided reads on the graph With option "-t coverage": outputs an equivalent graph removing uncovered edges and adding:
- for each node: the coverage per sample and per position for each edge: the number of mapped reads per sample using this edge
With option -t modify: outputs the same simplified graph:
- removing low covered edges and nodes (less that min_coverage) then phasing simple non branching paths
If -M option is specified, the input is considered as a Mapsembler output - thus composed of multiple independant graphes
MANDATORY
- -t <type>
- "c" "coverage" "m" "modify"
-
-o file_name: write obtained graph. Default: standard output
- -k size_seed: will use seeds of length size_seed. Default: 25.
- -c min_coverage: Will consider an edge as coherent if coverage (number of reads from all sets using this edge) is at least min_coverage. Default: 2
- -d max_substitutions: Will map a read on the graph with at most max_substitutions substitutions. Default: 1
- -k size_seed: will use seeds of length size_seed. Default: 25.