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Software for taxonomic assignment?

Bioinformatics Asked on December 1, 2020

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.

2 Answers

You could take a look at kraken2 It should fit your purpose.

Correct answer by Mr_Z on December 1, 2020

If you like blast, maybe you can try DIAMOND - the authors claim it's much faster than BLAST.

Answered by aLbAc on December 1, 2020

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