Usage: bwa mem [options] <in1.fq> [in2.fq]

Algorithm options:
-w INT band width for banded alignment [100]
-d INT off-diagonal X-dropoff [100]
-r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
-y INT seed occurrence for the 3rd round seeding [20]
-c INT skip seeds with more than INT occurrences [500]
-D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping cha

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