run_mappers - run a read mapper to map reads to reference
genomes
run_mappers NAMES READS -i REF -o OUT -m MAPPER
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).
- 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]