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abyss assembly and bubbles

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

abyss assembly
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updated by lauren.e.coombe • lauren.e.coombe • written by Phismil • Phismil

1 answer

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

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updated by GenoMax GenoMax • written by lauren.e.coombe • lauren.e.coombe

Thanks Lauren ! It was really helpful! Cheers

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written by Phismil • Phismil

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