[Bio-bwa-help] Parallel index construction

[Karel B. <kar...@gm...>]

Dear Heng,

thank you for your answer to my previous question.

I have one more question about BWA index construction. Is there currently
any possibility of how to parallelize this step? I am only aware of some
old discussion on this topic in this mailing list but maybe some new
solutions have appeared since then.

I construct the index in the following steps:

   1. bwa fa2pac
   2. bwa pac2bwt
   3. bwa bwtupdate
   4. bwa bwt2sa

Could pac2bwt or (fa2pac+pac2bwt) be parallelized with existing tools
(e.g., using RopeBWT2 or BWT-merge (https://github.com/jltsiren/bwt-merge))?

We are working with large metagenomic datasets so index construction time
really matters.

Thanks

Karel