sequences > 500 mb

[gribskov]

Is there any solution to the problem of reference sequnces > 500 Mb (wheat)?

[btpsj]

What part of BBTools are you trying to run that has this issue?

[gribskov]

Ah, this size limit is a known feature of BBMap. I think it has to do with packing words into 32 bits so i'm guessing it's hard to fix.

[btpsj]

@gribskov Brian recently added bbmap5.sh in some recent commits, which has a modified version of the BBMap algorithm and should be able to handle reference sequences ~ 1Gb. I've ran some simple tests but please give that a shot and let us know if that works for you or run into any additional issues.