What pipeline should I use to assemble bacterial genome?

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5.7 years ago

Seq225 ▴ 110

Hello,

I want to assemble bacterial genomes. The bacterial population was isolated from gut, and sequenced. Now I want to assemble the genomes and identify the population.

So, its a collection of bacteria and I need to assemble as well as identify them.

What are the best softwares/pipelines should I use?

Thanks.

sequencing assembly genome alignment • 1.5k views

ADD COMMENT • link 5.7 years ago by Seq225 ▴ 110

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You will want to look for metagenomic assembly tools such as metaSPAdes, (most popular assemblers now have a ‘meta’ version.

You can profile your sequence diversity with tools like Kraken/Bracken, Metaphlan and many many others.

I would start by looking for some up to date review articles.

ADD REPLY • link 5.7 years ago by Joe 21k

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Thank you very much. The sequences were assembled several years ago with CLC genomics workbench. I want to do the assembly again. Yes, I will read some recent reviews.

ADD REPLY • link 5.7 years ago by Seq225 ▴ 110

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MEGAHIT is fast and has modest memory requirements, it is a good option if you don't have access to powerful hardware.