mapsembler2_kissreads_graph1
Maps the provided reads on the graph
Overview
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
Options
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
History
- Debian 13 (Trixie) to Debian 10 (Buster): the text shown here
- Debian 9 (Stretch)