This is the command run_mappers that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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]
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