Usage: bwa aln [options] <in.fq>

Options: -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
-o INT maximum number or fraction of gap opens [1]
-e INT maximum number of gap extensions, -1 for disabling long gaps [-1]
-i INT do not put an indel within INT bp towards the ends [5]
-d INT maximum occurrences for extending a long deletion [10]
-l INT seed length [32]
-k INT maximum difference

This is a companion discussion topic for the original entry at quay.io/collaboratory/dockstore-tool-bwa-aln