Bowtie2 and bwa *big* disparity in alignment percentages

Question

[shubhra.bhattacharya]

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

Answer 1

[Istvan Albert]

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

[shubhra.bhattacharya]

Sure I'll try this out!