Best processing for finishing Eukaryotic genomes?
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4.2 years ago
stacy734 ▴ 40

Hi all, I am assembling some eukaryotic genomes, and trying different methods for finishing. I normally start with Spades, followed by a manual contig alignment and additional joins.

Does anyone have a favorite program for genome finishing? It doesn't need to be free. I have tried CLC workbench but it is not designed for eukaryotic genomes and runs out of memory.

Thanks for any advice.

Eukaryotic genome Assembly finishing • 1.0k views
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have a look to some of the gapclosing/gapfilling tools as well as polishing tools (Pilon, Arrow, ...) or "scaffolding" tools (AGOUTI, ... )

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Thanks Lieven! I appreciate your advice.

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out of interest (and hopefully without ending up in a philosophical debate) : what do you consider by 'genome finishing' ?

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Improving the assembly as much as possible. Making new joins, allowing manual review of joins and trimming junky stuff. I still expect a draft genome at the end, maybe just a better one.

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Spades for eukaryotes?

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depends on the genome size indeed, works pretty well for the smaller ones (some algae for example), would indeed not advise it for larger ones (30Gb conifer genomes for instance )

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True, I didn't think of algae and friends...

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I was using it for yeast. A small genome for a eukaryote.

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