Run BOWTIE on an set of input files (query) vs a database index.
The (basename of the) bowtie database to use.
Fastq input files - reverse
Bam output file
extra parameters to feed to bowtie
Format of the input files
Keep unmapped reads, unsorted BAM - takes up a lot of space!
Maximum allowed insertsize
Minimum allowed insertsize
orientation of the reads, allowed values are fr, rf, ff