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