run_mappers1
Run a read mapper to map reads to reference genomes
Usage
run_mappers NAMES
READS
-i
REF
-o
OUT
-m
MAPPER
Overview
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]
Releases
Unchanged in 6 releases since Debian 8 (Jessie).