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molikd / otb

Only The Best (Genome Assembly Tools)
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Build out bwa mem short read aligner container #34

Closed Astahlke closed 2 years ago

Astahlke commented 2 years ago

Need to build out bwa mem container https://github.com/lh3/bwa for #33

molikd commented 2 years ago

Hmm. I dunno, we should still be able to use minimap2 for short reads.

molikd commented 2 years ago

https://github.com/molikd/otb/commit/45b9d2352f373cf27242223eda03d47382950236 should fix this, needs testing before issue is closed.

Astahlke commented 2 years ago

Disagree! Minimap can handle short reads, but Hi-C are their own animal. Check out https://github.com/lh3/minimap2/issues/256 and https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa. The more recently updated readme of HiLine also recommends bwa-mem over minimap https://github.com/wtsi-hpag/HiLine

molikd commented 2 years ago

grr. I spent some time looking at weather we could use Nucmer or Unimap as well, just because I already have containers for those, no dice.

molikd commented 2 years ago

added bwa-mem2 for this in 713c771 all subsequent commands are switched over, and prefetch, checks are made as well.