---
name: "run_mappers"
section: "1"
platform: "linux"
package: "gasic"
version: "0.0.r19-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/run_mappers"
---

# run\_mappers(1)

run a read mapper to map reads to reference genomes

## NAME

run\_mappers - run a read mapper to map reads to reference genomes

## SYNOPSIS

**run\_mappers** *NAMES READS -i REF -o OUT -m MAPPER*

## DESCRIPTION

Run a read mapper to map reads to reference genomes.

The names in the NAMES file will be inserted in the provided string patterns. Each pattern must contain exactly one "%s" placeholder (python string formatting).

## OPTIONS

- *NAMES*

  Filename of the names file; the plain text names file should contain one name per line. The name is used as identifier in the whole algorithm.

- *READS*

  File containing the reads to be mapped.

- **-h**, **--help**

  show this help message and exit

- **-m** MAPPER, **--mapper**=*MAPPER*

  Identifier of mapper defined in core/tools.py \[default: none\]

- **-i** REF, **--index**=*REF*

  Pattern, that points to the reference sequences/indices when used with a name. Placeholder for the name is "%s". \[default: ./ref/%s.fasta\]

- **-o** OUT, **--output**=*OUT*

  Pattern, that points to the output SAM file, when used with a name. Placeholder for the name is "%s". \[default: ./SAM/%s.sam\]