Answers.Body: <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>
  
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Answers.CreationDate: 2020-08-14T09:57:18.637Z
Answers.LastActivityDate: 2020-08-14T09:57:18.637Z
Answers.UserDisplayName: aLbAc
Answers.Body: <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>
  
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Answers.CreationDate: 2020-08-12T21:04:26.637Z
Answers.Text: yes, kraken2 performed well in an independant benchmark https://lemmi.ezlab.org/
Answers.UserDisplayName: Chris_Rands
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Answers.CreationDate: 2020-08-14T09:52:13.263Z
Answers.Text: It does work well, but it's less accurate at lower taxonomic ranks (as most tools are)
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Answers.UserDisplayName: Mr_Z
Body: <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>
  
Tags: <blast><metagenome><taxonomy>
Title: Software for taxonomic assignment?
ThreadText: # Software for taxonomic assignment?
  
  (Asked by: username_0 on 2020-08-12)
  
  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.
  
  **Tags:** blast, metagenome, taxonomy
  
  
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  ## 2 answers
  
  ### Answer by username_2 on 2020-08-12. Score: 4 | Accepted answer
  
  You could take a look at [kraken2](https://ccb.jhu.edu/software/kraken2) It should fit your purpose.
  
  > **Comments:**
  > **username_3**: yes, kraken2 performed well in an independant benchmark https://lemmi.ezlab.org/  
  > **username_1**: It does work well, but it's less accurate at lower taxonomic ranks (as most tools are)  
  
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  ### Answer by username_1 on 2020-08-14. Score: 3
  
  If you like blast, maybe you can try [DIAMOND](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/diamond/) - the authors claim it's much faster than BLAST.
  
  
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