Question: Bowtie2 and bwa *big* disparity in alignment percentages
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gravatar for shubhra.bhattacharya
23 months ago by
shubhra.bhattacharya120 wrote:

Dear all, I have aligned my 300*2 data against a 4 Mb reference using both Bowtie2 and bwa-0.7.

The alignment percentage observed in bowtie2 is 80% and with bwa it is 99%. What is fundamentally different causing such a large difference between the aligners.

The coverage once calculated from the mpileup drops tp 1% at 20x. So, the depth is low in both the methods. But bwa has a better horizontal coverage in terms of alignment but depth drops in this too.

Thanks

alignment • 452 views
ADD COMMENTlink modified 23 months ago by Istvan Albert ♦♦ 84k • written 23 months ago by shubhra.bhattacharya120
0
gravatar for Istvan Albert
23 months ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

This is because by default the two aligners are set up to run differently.

To produce equivalent alignments try:

bowtie2 --very-sensitive-local

or if feeling adventourous:

bowtie2 -D 20 -R 3 -N 1 -L 20

Beyond that the changes run deeper than just how many alignments are produced. I have a chapter on this in the Biostar Handbook (not a free resource): https://www.biostarhandbook.com/align/compare-aligners.html

ADD COMMENTlink written 23 months ago by Istvan Albert ♦♦ 84k

Sure I'll try this out!

ADD REPLYlink written 23 months ago by shubhra.bhattacharya120
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