Question: BWA vs. bowtie
gravatar for blur
2.1 years ago by
European Union
blur110 wrote:

Hi, I have been trying to align a specific library, and I used both Bowtie2 and BWA. BWA gives much higher alignment rates, and I am wondering if it is due to bad parameters on my side, bad bowtie version, or something else.

I am running local alignment: bowtie2 -x ref --local -L 6 -p 4 -1 r1.fq -2 r2.fq > out.sam and then tried global alignment

BWA mem ref r1.fq r2.fq > out.sam

Does anyone have an idea? Thanks,

bwa ngs bowtie2 • 1.4k views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan94k • written 2.1 years ago by blur110
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

In cases where you really need local alignment, bowtie2 tends to only give good results with --very-sensitive-local, rather than just --local. I worry that your use of -L 6 with any reasonable value of -D is going to result in bowtie2 performing poorly. Instead, try the defaults for --very-sensitive-local and maybe tweak from there if you want to bother going through the effort.

ADD COMMENTlink written 2.1 years ago by Devon Ryan94k

I ended up using BWA. Though using your ideas improved the bowtie alignment greatly, BWA was still much better Thanks

ADD REPLYlink written 2.1 years ago by blur110
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: 1836 users visited in the last hour