abyss assembly and bubbles

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Arsalan Emami-Khoyi

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Feb 22, 2020, 2:36:23 PM2/22/20
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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

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Feb 24, 2020, 2:02:26 PM2/24/20
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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

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Feb 24, 2020, 2:08:52 PM2/24/20
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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

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Feb 25, 2020, 11:57:10 AM2/25/20
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Many thanks Lauren!
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