BWA vs. bowtie

Question

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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,

Answer 1

[Devon Ryan]

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.

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