Provided by: mapsembler2_2.2.4+dfsg-3build1_amd64
mapsembler2_kissreads_graph - maps the provided reads on the 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]
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 independent graphes
MANDATORY -t <type> "c" "coverage" "m" "modify" OPTIONAL -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
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.