Taxonomic annotation of selected genes

Question

[tpellegrinetti]

Hi all, I have several short-read metagenomes (HiSeq) that I am working. I would like to assess the taxonomy associated to some biogeochemical genes by using reads approaches.

I know to do this with MG-RAST or using DIAMOND+MEGAN with a custom gene database (NCBI - protein fasta). Someone know other ways to perform this taxonomic annotation of a particular gene?

Thank you.

Answer 1

[lieven.sterck]

Kraken(2) ?

https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46

there is another as well, but can't get to the name right now

[GenoMax]

centrifuge - https://ccb.jhu.edu/software/centrifuge/

[tpellegrinetti]

Thank you lieven.sterck.

Kraken is a really good way. Do you know if the best way is using a custom gene database? Is there an easy way to do this gene database other than by NCBI?

thanks.

[lieven.sterck]

if you have no clue where those reads might come from (taxonomically) you're best of to use an as comprehensive as possible DB, something like NCBI nr indeed . If you can subset if a priori then you can consider a more specific DB.

an "alternative' to NCBI nr, might be uniprot/Trembl/ ...