Question: fixing human ref genome random access memory
gravatar for SurdanBurasi
4 weeks ago by
SurdanBurasi0 wrote:

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

linux bwa memory usage ngs • 79 views
ADD COMMENTlink modified 4 weeks ago by Devon Ryan94k • written 4 weeks ago by SurdanBurasi0
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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.

ADD COMMENTlink written 4 weeks ago by Devon Ryan94k

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

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by ATpoint31k

That's a happy update :)

ADD REPLYlink written 4 weeks ago by Devon Ryan94k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1263 users visited in the last hour