Question: Best processing for finishing Eukaryotic genomes?
0
gravatar for stacy734
7 days ago by
stacy73440
stacy73440 wrote:

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.

ADD COMMENTlink written 7 days ago by stacy73440

have a look to some of the gapclosing/gapfilling tools as well as polishing tools (Pilon, Arrow, ...) or "scaffolding" tools (AGOUTI, ... )

ADD REPLYlink modified 6 days ago • written 7 days ago by lieven.sterck7.8k

Thanks Lieven! I appreciate your advice.

ADD REPLYlink written 7 days ago by stacy73440

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

ADD REPLYlink modified 6 days ago • written 6 days ago by lieven.sterck7.8k

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.

ADD REPLYlink written 1 day ago by stacy73440

Spades for eukaryotes?

ADD REPLYlink written 6 days ago by cschu1812.3k

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 )

ADD REPLYlink written 6 days ago by lieven.sterck7.8k
1

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

ADD REPLYlink written 5 days ago by cschu1812.3k

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

ADD REPLYlink written 1 day ago by stacy73440
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