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]