Can anyone explain how the builds and references should be set in BBSplit?
I have a set of reads that I would like to compare against the target genome and two other contaminant genomes. Can these all be created as one ref directory, each separate or one for target and one for contaminant? If multiple builds are generated should each of these be called in the command line e.g ./bbsplit.sh build=1 build=2 in=reads1.fq in2=reads2.fq ref_x=target.fa ref_y=contam_1.fa,contam2.fa
If anyone has an idea that would be a great help, thanks!