table of contents
| MAPSEMBLER2_KISSREADS_GRAPH(1) | User Commands | MAPSEMBLER2_KISSREADS_GRAPH(1) |
NAME¶
mapsembler2_kissreads_graph - manual page for mapsembler2_kissreads_graph 2.2.3+dfsgDESCRIPTION¶
NAME ./kissreads_graph/mapsembler2_kissreads_graph, version 1.0.0 Beta - Copyright INRIA - CeCILL License-h prints this message and exit
USAGE ./kissreads_graph/mapsembler2_kissreads_graph input_graph <readsC1.fasta/fastq[.gz]> [<readsC2.fasta/fastq[.gz]> [<readsC3.fasta/fastq[.gz] ...] -M -t type [-k value] [-c min_coverage] [-d max_substitutions] [-o name] [-h]
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"
OPTIONS -M: the input is considered as a Mapsembler output
-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
SEE ALSO¶
The full documentation for mapsembler2_kissreads_graph is maintained as a Texinfo manual. If the info and mapsembler2_kissreads_graph programs are properly installed at your site, the command- info mapsembler2_kissreads_graph
should give you access to the complete manual.
| September 2016 | mapsembler2_kissreads_graph 2.2.3+dfsg |