Question: fixing human ref genome random access memory
0
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
0
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
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