Which metagenomics tool works best?

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6.1 years ago

Seq225 ▴ 110

Hi,

I have paired end illumina reads from multiple sources. I want to study the metagenomics. Which tool would be best? I can see people are using MEGAN, Kraken, Centrifuge more than the other tools.

My main objective is to compare the metagenomics population across my samples.

Thanks!

alignment genome sequencing assembly metagenomics • 2.3k views

ADD COMMENT • link 6.1 years ago by Seq225 ▴ 110

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Kraken and Centrifuge have close results, please refer also to this blog https://www.sevenbridges.com/centrifuge/

ADD REPLY • link 6.1 years ago by Medhat 9.8k

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Thank you. I have actually read this today. Looks like I can use either one.

ADD REPLY • link 6.1 years ago by Seq225 ▴ 110

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I like centrifuge better since you get the number of reads that are uniquely classified to a certain genomic sequence. This is likely to be more specific. So if you are doing comparative genomics, this might be what you want. MEGAN is great too, however, it is slower compared to the other tools. But it provides functional analysis of datasets which is beyond simple taxonomy.