Reference database for shotgun metagenomics

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5.5 years ago

mrudhulaks • 0

Hi,

I am currently working on understanding the relation between gut microbiome and cognition. We would like to perform shotgun metagenomics analysis. I am a bit sceptical about the availability of bacterial reference database. Could you please let me know 1) Which is the best reference database for bacterial metagenomics. 2) What is the workflow for shotgun metagenomics.

Thank you

sequencing next-gen Assembly • 1.5k views

ADD COMMENT • link updated 5.5 years ago by Biostar 20 • written 5.5 years ago by mrudhulaks • 0

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Have you looked at HUMAnN2?

ADD REPLY • link 5.5 years ago by GenoMax 141k

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Thank you for the comment. I have not worked on HUMAnN2. I am interested in species/strain level information. Do you suggest HUMAnN2 would be the best choice? Thank you

ADD REPLY • link 5.5 years ago by mrudhulaks • 0

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You're right to be sceptical. I have spent a long time working in and around this area. In any rate, it is a lot more robust than 16S.

Nonetheless, I would always assess bacterial shotgun metagenomes with multiple tools and databases. Also, BLAST analysis can be helpful. Finally, controls are incredibly important, especially for low-biomass samples.

ADD REPLY • link 5.5 years ago by colindaven 6.4k

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