---
name: "mapsembler"
section: "1"
platform: "linux"
package: "mapsembler2"
version: "2.1.6+dfsg-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/mapsembler"
---

# mapsembler(1)

manual page for mapsembler 2.1.6+dfsg

## NAME

mapsembler - manual page for mapsembler 2.1.6+dfsg

## DESCRIPTION

NAME mapsembler, version 2.0.5.deb - Copyright INRIA - CeCILL License

SYNOPSIS ./maps/mapsembler \<starters.fasta\> \<readsC1.fasta\> \[\<readsC2.fasta\> \[\<readsC3.fasta\] ...\] \[-E\] \[-t extension\_type\] \[-q value\] \[-k value\] \[-c value\] \[-d authorized\_distance\] \[-e error\_threshold\] \[-g value\] \[-i index\_name\] \[-o name\] \[-m name\] \[-h\]

DESCRIPTION

-

  Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.

OPTIONS

**-E** Extend only: avoid the mapping+substarter generation phase

**-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

**-q** size\_seed: will use seeds of length size\_seed during the mapping process. Default: 25, value should be in \[5-31\]

**-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

**-d** authorized\_distance: a substarter is distant by at most authorized\_distance substitutions. Default: 2

**-e** error\_threshold: a nucleotide is corrected if occurs less than error\_threshold times. 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

**-n** node\_len: limit max of nodes length. Default: 1000000

**-l** 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 LARGEUR or PROFONDEUR. Default: LARGEUR

**-m** file\_name: write in file "file\_name" the reads mapped on starters

**-h** prints this message and exit

## SEE ALSO

The full documentation for **mapsembler** is maintained as a Texinfo manual.  If the **info** and **mapsembler** programs are properly installed at your site, the command

-

  **info mapsembler**

should give you access to the complete manual.