About runing Pilon on individual chromosomes when polish draft genome assembly

Question

[boymin2020]

Hi all,

Recently I have been working on genome assembly for several species on my own server (1TB ram, 128cores, and enough internal storage). My problem is that when the estimated genome size is more than 2.5GB, the PILON software which is used for polish draft genome assembly was stopped because of insufficient memory.

One of my solutions is to split the whole draft genome assembly by chromosomes followed by polish by PILON, then concentrate the polished chromosomes into a big one. Here I want to know any possible issues by doing in this way.

Thanks,

Answer 1

[Istvan Albert]

Since pilon uses alignments as a guide, as long as you performed the alignments on the entire genome I believe there won't be substantial problems with your approach.

[boymin2020]

thanks for your reply. I do have not encountered any substantial problems so far. I am just confused about the RAM requirement of PILON.

[sansan96]

Hello,

What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing the entire genome.

Thanks so much.