<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>

CC BY-SA 4.0
2020-08-14T09:57:18.637Z
2020-08-14T09:57:18.637Z
aLbAc
<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>

CC BY-SA 4.0
2020-08-12T21:04:26.637Z
yes, kraken2 performed well in an independant benchmark https://lemmi.ezlab.org/
Chris_Rands
CC BY-SA 4.0
2020-08-14T09:52:13.263Z
It does work well, but it's less accurate at lower taxonomic ranks (as most tools are)
aLbAc
CC BY-SA 4.0
2020-08-12T19:18:47.967Z
2020-08-12T19:18:47.967Z
Mr_Z
<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>

<blast><metagenome><taxonomy>
Software for taxonomic assignment?
# 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

---

## 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)  

---

### 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.


---

