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

# mapsembler\_extend(1)

extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly

## NAME

mapsembler\_extend - extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly

## SYNOPSIS

**mapsembler\_extend** \<extrem\_kmers.fasta\> \<readsC1.fasta\> \[\<readsC2.fasta\> \[\<readsC3.fasta\] ...\] \[-t extension\_type\] \[-k value\] \[-c value\] \[-g value\] \[-i index\_name\] \[-o name\] \[-h\]

## DESCRIPTION

Mapsembler 2 extends a DNA sequence of interest given a set of reads, by computing a targeted micro assembly.

## OPTIONS

**-t** extension\_type. Default: 1

-

  1: a strict sequence: any branching stops the extension

-

  2: a consensus sequence: contiging approach

-

  3: a strict graph: any branching is conserved in the graph

-

  4: a consensus graph: "small" polymorphism is merged, but "large" structures are represented

**-k** size\_kmers: Size of the k-mers used duriung the extension phase Default: 31. Accepted range, depends on the compilation (make k=42 for instance)

**-c** min\_coverage: a sequence is covered by at least min\_coverage coherent reads. Default: 2

**-g** estimated\_genome\_size: estimation of the size of the genome whose reads come from.

-

  It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion

**-x** node\_len: limit max of nodes length. Default: 40

**-y** graph\_max\_depth: limit max of graph depth.Default: 10000

**-i** index\_name: stores the index files in files starting with this prefix name. Can be re-used latter. Default: "index"

-

  IF THE FILE "index\_name.bloom" EXISTS: the index is not re-created

**-o** file\_name\_prefix: where to write outputs. Default: "res\_mapsembler"

**-p** search\_mod: kind of prosses Breadth or Depth. Default: Breadth

**-h** prints this message and exit

## AUTHOR

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