---
name: "mapsembler2_extremities"
section: "1"
platform: "linux"
package: "mapsembler2"
version: "2.2.4+dfsg1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mapsembler2_extremities"
---

# mapsembler2\_extremities(1)

performs the first step of Mapsembler2\_extend

## NAME

mapsembler2\_extremities - performs the first step of Mapsembler2\_extend

## SYNOPSIS

**mapsembler2\_extremities** **--k** \<kmersize\> **--starters** \<fasta\> **--reads** \<dataset\> **--output** \<substarterfile\> \[optional arguments\]

## DESCRIPTION

This modules performs the first step of Mapsembler2\_extend. For each starter, it outputs a list of extremities of the starter (of length \*k\*) are found in the reads, up to 1 indel or mismatch.

## OPTIONS

- **--k** (1 arg):

  kmer size that will be used for mapsembler2  \[default ''\]

- **--starters** (1 arg):

  starters fasta file  \[default ''\]

- **--reads**(1 arg):

  reads dataset file name. Several reads sets can be provided, surrounded by "'s and separated by a space (e.g. **--reads** "reads1.fa reads2.fa")  \[default ''\]

- **--output** (1 arg):

  output substarters file name  \[default ''\]

- **--min-solid-subkmer** (1 arg):

  minimim abundance to keep a subkmer  \[default '3'\]

- **-debug** (0 arg):

  debugging

- **-nb-cores** (1 arg):

  number of cores  \[default '0'\]

- **-verbose** (1 arg):

  verbosity level  \[default '1'\]

- **-help** (0 arg):

  display help about possible options

## AUTHOR

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