Entering edit mode
3.9 years ago
stacy734
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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.
have a look to some of the gapclosing/gapfilling tools as well as polishing tools (Pilon, Arrow, ...) or "scaffolding" tools (AGOUTI, ... )
Thanks Lieven! I appreciate your advice.
out of interest (and hopefully without ending up in a philosophical debate) : what do you consider by 'genome finishing' ?
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.
Spades for eukaryotes?
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 )
True, I didn't think of algae and friends...
I was using it for yeast. A small genome for a eukaryote.