what's the best Kmer should be set when assembling bacteria genome

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4.3 years ago

zhangdengwei ▴ 210

Hi all,

I am new to bacterial genome assembly. Now I'd like to assemble a batch of single bacteria genome using Spades or IDBA-UD or Megahit. So I have no idea about which is better and how to set the best Kmer for assembly. Any suggestions would be greatly appreciated!

genome assembly Kmer • 1.4k views

ADD COMMENT • link 4.3 years ago by zhangdengwei ▴ 210

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There's no single best option as it depends on the bacterium.

You might be interested in using something like shovil (a wrapper/front end around spades) which will try several kmer options and assess the best.

ADD REPLY • link 4.3 years ago by Joe 21k

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Assembly is an art, usually the default works good. Anyway I would use an established pipeline like https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007134 or https://github.com/nf-core/bacass

ADD REPLY • link 4.3 years ago by Asaf 10k

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I entirely agree with you that assembly is an art. I tried several assemblers with different parameters, I would get different results. For example, I could obtain longer N50 with unicycler than with spades, but it came at a cost of shorter total assembly length. In general, it seems spades outperform others, at least according to my experience.