---
name: "run_mapsembler2_pipeline"
section: "1"
platform: "linux"
package: "mapsembler2"
version: "2.2.4+dfsg1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/run_mapsembler2_pipeline"
---

# run\_mapsembler2\_pipeline(1)

pipelines the mapsembler2 tools

## NAME

run\_mapsembler2\_pipeline - pipelines the mapsembler2 tools

## SYNOPSIS

**run\_mapsembler\_and\_phaser.sh** *-s \<starter.fasta\> -r \<reads.faste\> -t* \[*1/2/3/4*\]*\<options\>*

## DESCRIPTION

run\_mapsembler\_pipeline.sh, a pipelining mapsembler2\_extremities, mapsembler2\_extend and kissread\_g

## OPTIONS

**-s**: file containing starters (fasta)

**-r** list of reads separated by space, surrounded by the '"' character. Note that reads may be in fasta or fastq format, gzipped or not. Example: **-r** "data\_sample/reads\_sequence1.fasta   data\_sample/reads\_sequence2.fasta.gz".

**-t**: kind of assembly: 1=unitig (fasta), 2=contig (fasta), 3=unitig (graph), 4=contig(graph)

### OPTIONAL

**-p** prefix. All out files will start with this prefix. Example: **-p** my\_prefix

**-k** value. Set the length of used kmers. Must fit the compiled value. Default=31. Example **-k** 31

**-c** value. Set the minimal coverage. Default=5. Example **-c** 5

**-d** value. Set the number of authorized substitutions used while mapping reads on found SNPs. Default=1. Example: **-d** 1

**-g** value. Estimated genome size. Used only to control memory usage. e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10 million. Example: **-d** 10000000

**-f** value. Set the process of search in the graph (1=Breadth  and 2=Depth). Default=1. Example: **-f** 1

**-x** value. Set the maximal nodes length . Default=40. Example: **-x** 40

**-y** value. Set the maximal graph depth . Default=10000. Example: **-y** 10000

**-h** Prints this message and exist

## SEE ALSO

Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr

## AUTHOR

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