POLL - BWA vs Bowtie 2

[Sequencing.com]

Is anyone still using BWA or have almost all switched to Bowtie 2?

Our bioinformatics team has been evaluating both. BWA is quite slow (and resource hungry) compared to Bowtie 2 although there is a rogue contingent amongst us that are still BWA supporters.

We decided to turn to SEQanswers to see what everyone else thinks - do you use BWA or Bowtie 2?

Appreciate your input!
Irene
Sequencing.com

[Brian Bushnell]

Well gosh, I've already moved on to BBMap.

[Sequencing.com]

Hi Brian - nice to meet you! Our team actually just started evaluating BBMap and it's nice to see such optimized code. It's made a great first impression on us so far and we'll provide feedback once we had a chance to conduct some comparison testing.

Irene

[Brian Bushnell]

That's good to hear. As for bwa versus Bowtie2 - I don't like bwa-aln much, but bwa-mem in my tests is much faster than Bowtie2.

[luc]

Another BBmap vote - it is very fast already at the default settings, very easy to use, offers tons of options.

[Richard Finney]

I vote novoalign.

People sometimes benchmark this stuff.
Is there a good recent review of the merits of the various aligners?

[luc]

Hi Richard,

this site aims to do this (except speed comparisons):

http://www.bioplanet.com/gcat/

e.g.:

http://www.bioplanet.com/gcat/reports/1257-hvdlenkzth/alignment/100bp-se-small-indel/cushaw3/compare-26-35

I have not checked lately, but there was at least a slight theoretical problem that the test files were generated with the read simulator originating from the bwa aligner. The playing field will never be perfectly balanced.

Also:

http://genomespot.blogspot.com/2014/11/dna-aligner-accuracy-bwa-bowtie-soap.html

[holmrenser]

We use bwa mem mostly, but I think we still use bowtie2 for cufflinks/tophat/etc.
I recently started using BBMap and am impressed, although there is nothing to cite yet!

[Ahaswer]

Hello, I'm using bowtie2, however my collegue praises BWA. Also I have to try BBmap and compare results between those three.