Run SMALT on an set of input files (query) vs a database index.
The (basename of the) smalt database to use.
reference fasta file
fastq input files directory - reverse
output BAM file (automatically converted & filtered for reads that to not map)
extra parameters to feed to smalt
Maximum allowed insertsize
Minimum allowed insertsize
output format (sam or samsoft)
pair type (pe: fr/illumina short; mp: rf/illumina mate pairs or pp: ff
No threads to use