Responses to question about functional annotation of metagenomic reads

Posted a question to a few placesHi. 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, 2023Humann suggestion  fraggenescan on the raw reads, then use hmmer w/ pfam-A or kegg hmm.EggNog MapperMGRASThttp://mgrast.orgMetawrapYooseph approachhttps://pubmed.ncbi.nlm.nih.gov/27400380/https://pubmed.ncbi.nlm.nih.gov/27585568/mi-faserhttps://bromberglab.org/project/mifaser/ …MGXhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0460-1 …MMseqs or DiamondSqueeze Metahttps://github.com/jtamames/SqueezeMetaMetageni/Superfocushttps://github.com/metageni/SUPER-FOCUSPlasshttps://github.com/metageni/SUPER-FOCUSMegan + Diamondhttps://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.59MetAnnotatehttps://github.com/MetAnnotate/MetAnnotateReview of relevancehttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6289-6UPROChttps://pubmed.ncbi.nlm.nih.gov/25540185/Looking Glasshttps://www.nature.com/articles/s41467-022-30070-8ShortbredProteinfer / MGnifyhttps://www.ebi.ac.uk/metagenomics/pipelines/2.0AntiSmashMMseq2 -------- This is from the" Tree of Life Blog " of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter...
Source: The Tree of Life - Category: Microbiology Source Type: blogs