mapsembler2_kissreads_graph1
Maps the provided reads on the graph
Usage
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]
Overview
mapsembler2_kissreads_graph maps the provided reads on the graph With option "-t coverage": outputs an equivalent graph removing uncovered edges and adding:
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for each node: the coverage per sample and per position |
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for each edge: the number of mapped reads per sample using this edge |
With option "-t modify": outputs the same simplified graph:
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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>
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"c" "coverage" |
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"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
Releases
5 releases since Debian 9 (Stretch); the text changed 1 time.