text: user4401: I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable phylogenetic marker, where present, but the scale of my current dataset makes it a bit daunting.
  Is there any software for taxonomic assignment that you could recommend? It's fine if it requires command line use. There are so many options listed online that I didn't even know where to start... Please and thank you.
  
  user2245: If you like blast, maybe you can try DIAMOND - the authors claim it's much faster than BLAST.
  
  user3360: You could take a look at kraken2 It should fit your purpose.
  
original_text: 4401: <p>I have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I already know to be reliable phylogenetic marker, where present, but the scale of my current dataset makes it a bit daunting.</p>
  <p>Is there any software for taxonomic assignment that you could recommend? It's fine if it requires command line use. There are so many options listed online that I didn't even know where to start... Please and thank you.</p>
   2245: <p>If you like blast, maybe you can try <a href="https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/diamond/" rel="nofollow noreferrer">DIAMOND</a> - the authors claim it's much faster than BLAST.</p>
   3360: <p>You could take a look at <a href="https://ccb.jhu.edu/software/kraken2" rel="nofollow noreferrer">kraken2</a> It should fit your purpose.</p>
  