A fast bam file deduplicator.
This tool deduplicates bam files FAST.
It treats all paired reads as such and considers a duplicate to have both reads R1 and R2 the same genomic position and length, but keeps the ones with the max sum of quality scores.
doopa uses 8 threads by default because it maxes out in performance using 800% cpu load, so there's not much point giving it more threads.
GPLv3+