Entering edit mode
2.5 years ago
tpellegrinetti
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0
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.
centrifuge- https://ccb.jhu.edu/software/centrifuge/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.
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/ ...