abyss assembly and bubbles

Question

[Phismil]

Dear Colleagues,

We are assembling an insect genome from a large pool of different individuals.

As an artefact of pool sequencing, we have a large number of polymorphisms that end up as bubbles in the assembly graph.

I am wondering if any of developers and/or experienced users recommend any specific advance settings in Abysse2 that could potentially mitigate this issue?

Many thanks in advance

Answer 1

[lauren.e.coombe]

Hi Arsalan,

If you would like to get more efficient bubble popping, we have used these parameters for PopBubbles in the past for highly heterozygous samples, so it would be worth a try for your pool:

POPBUBBLES_OPTIONS='--scaffold -a 4'

Hope that helps! Lauren

[Phismil]

Thanks Lauren ! It was really helpful! Cheers