Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
SNPsplit - Allele-specific alignment sorting for N-masked genomes fkrueger Bioinformatics 2 08-19-2015 05:37 AM
No. of threads for alignment dena.dinesh RNA Sequencing 1 11-12-2014 07:12 AM
Should jo manager threads match tool threads? Studentlost RNA Sequencing 0 10-25-2014 11:00 AM
Alignment & visualisation of two similar contigs TabeaK Bioinformatics 2 07-18-2013 03:43 PM
Valid alignment & Uniqueness_bowtie liu_xt005 Bioinformatics 0 12-14-2012 02:30 PM

Thread Tools
Old 11-27-2017, 11:36 AM   #1
Location: VA

Join Date: Jul 2011
Posts: 17
Question Optimal balance of threads for alignment & sorting?

Hello all,

I was wondering if anyone knows the optimal way to assign threads for alignment and bam decompression/sorting.
I'm running some alignments and then sorting and de-duping the alignments using a single command like so:

bwa mem -t 70 ref.fasta reads_R1.fq.gz reads_R2.fq.gz \
| samblaster \
| sambamba view -S -f bam /dev/stdin \
| sambamba sort -t 70 -m 50G -o out.bam /dev/stdin

There are 72 cores on our server. The read files are large, and this command took about 6hrs to run.

I then tried it a different way, wherein instead of giving 70 threads to both the alignment and sorting, I gave 50 threads to BWA and 20 to sambamba. That second attempt shaved about 20 minutes off the run (a little over 5.5hrs). This makes me think there is something going on that I don't understand about how the threads are assigned to different processes, and that they must somehow be getting in each other's way.

I thought about running it with a bunch of different combinations (perhaps with a small subset) to see what the best distribution was, but before doing that it seemed sensible to search for the answer first. Google has not been my friend so far on this, so I though I would see if anyone here knows the optimal way to assign threads for alignment and sorting.

A. Koeppel
afkoeppel is offline   Reply With Quote

alignment, multithreading, sambamba

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:57 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO