Tools for raw reads that estimate the percentage of reads that hit marker genes using protein BLAST or more advanced approaches based on protein HMM profiles of marker PFAM domains

Question

[shevch2009]

Hello, all!

I am looking for some tools, specifically for raw reads (shougun) that estimate the percentage of reads that hit marker genes using protein BLAST or more advanced approaches based on protein HMM profiles of marker PFAM domains. Are there any pipelines for this kind of aim?

I got an advice to use humann, but it's not working, I have opened the topic - https://forum.biobakery.org/t/errors-with-humann-metaphlan/8447

But, it looks like there will be no responses, and the issue is not new.

Most of tools I have checked - workes on mags or contigs only.

I would appreciate any suggestions,

Thanks, Best, Alla

[GenoMax]

If you just want fast translated sequences you could use DIAMOND (https://github.com/bbuchfink/diamond ) as long as you have the necessary resources available.