---
name: "mapsembler2_kissreads_graph"
section: "1"
platform: "linux"
package: "mapsembler2"
version: "2.2.4+dfsg1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mapsembler2_kissreads_graph"
---

# mapsembler2\_kissreads\_graph(1)

maps the provided reads on the graph

## NAME

mapsembler2\_kissreads\_graph - maps the provided reads on the graph

## SYNOPSIS

**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

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

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.