abyss assembly and bubbles

[Arsalan Emami-Khoyi]

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

The same topic was posted on biostars per recommendation available at : https://www.biostars.org/p/422930/

[Lauren Coombe]

Hi Arsalan,

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

[Lauren Coombe]

To clarify -- if you would like to have more efficient bubble popping for your assembly, we'd suggest using those parameters. ABySS outputs a haploid assembly, so will choose one of the bases to include in the scaffold as part of the bubble popping.

[Arsalan Emami-Khoyi]

Many thanks Lauren!