Add option to align multiple .fastq files at once? about bwa-mem2 HOT 2 CLOSED

Do you still need this?

from bwa-mem2.

Yes, I managed to hack together something that sort-of works for me personally, but I'd like to include it as part of a pipeline and it would be really nice to have an official solution.

Having a version that let's you batch multiple single or paired end fastq files would be a good 90% solution.

I wound up making a solution that let's bwa-mem2 run as a daemon program aligning submitted jobs at any time, which is even better for my needs.

What I wasn't able to solve is making it produce the same results each time without restarting from scratch. In about 5-10% of alignments, it gives a different primary alignment. I don't think it's due to the random number generator calls in bwa-mem2 but is maybe due to either some aspect of threading or due to something about how the data structures are modified during alignment.

If you guys do make an official solution I would be very glad to use it.

from bwa-mem2.