fixing human ref genome random access memory

Question

[SurdanBurasi]

Can I fix the human reference genome file on physical random access memory so that the bwa program can process it from this fixed file? Can a secondary bwa execution also align using this file without ram getting a new file? my goal is to ensure the amount of time and low ram usage during writing on random acces memory

Answer 1

[Devon Ryan]

The only aligner I'm aware of that puts its index into shared memory like that is STAR, so no there is not currently a way to do this with BWA. Note that BWA is quite memory efficient, so unless you have a node with 100+ threads available but only say 20GB RAM you shouldn't have issues with multiple BWA processes swamping your memory.

[ATpoint]

The bowtie aligners and hisat2 do offer sm and are very memory-efficient.

[Devon Ryan]

That's a happy update :)