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/