Profiling taxonomic distribution of genes in human gut microbiome

Question

[dazhudou1122]

Dear Biostars community,

I am trying to determine the abundance and taxonomic distribution of a gene cluster in human gut microbiome samples (metagenomic sequencing). I would like to do this using blast (diamond blast). Can you give me suggestions on how to profile the taxonomic distribution of the mapped reads (from blast)? Or is there any existing pipeline that will allow me to achieve my goal?

Any information will be highly appreciated!

Best,

Wenhan

Answer 1

[Charles Warden]

If you subsample your reads (or, if you use PacBio CCS reads, maybe using all of your reads is OK), you can test using BLAST as an alternative genera assignment method.

I would have to learn more about Diamond BLAST, but I think mothur and the RDPclassifier (web-interface or command-line) are some good starting points (QIIME is also a popular option, but I don't think that I've tried the latest version).