Responses to question about functional annotation of metagenomic reads

Posted a question to a few places

Hi. We would like to functionally annotate some metagenomic sequencing reads without doing any assembly or binning or read mapping to reference genomes. Just annotate by searching things like nr, PFAM, COGs, etc. Anyone know of tools that do this?

— Jonathan Eisen (@phylogenomics) March 29, 2023

Humann suggestion

 

fraggenescan on the raw reads, then use hmmer w/ pfam-A or kegg hmm.

EggNog Mapper

MGRAST

http://mgrast.org

Metawrap

Yooseph approach

https://pubmed.ncbi.nlm.nih.gov/27400380/

https://pubmed.ncbi.nlm.nih.gov/27585568/

mi-faser

https://bromberglab.org/project/mifaser/…

MGX

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0460-1…

MMseqs or Diamond

Squeeze Meta

https://github.com/jtamames/SqueezeMeta

Metageni/Superfocus

https://github.com/metageni/SUPER-FOCUS

Plass

https://github.com/metageni/SUPER-FOCUS

Megan + Diamond

https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.59

MetAnnotate

https://github.com/MetAnnotate/MetAnnotate

Review of relevance

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6289-6

UPROC

https://pubmed.ncbi.nlm.nih.gov/25540185/

Looking Glass

https://www.nature.com/articles/s41467-022-30070-8

Shortbred

Proteinfer / MGnify

https://www.ebi.ac.uk/metagenomics/pipelines/2.0

AntiSmash

MMseq2