Viral Data classification

Question

[ARich]

Hi, I would like to classify my viral contigs could anyone recommend me the best way to that. Also if someone has created viral database for blast?

Thanks

Answer 1

[pld]

There are a few approaches, depending on how many you have and where your samples came from. The easiest would be to just blast them against nt and filter for viruses via taxid. If you have a large number of contigs, you may want to download the NCBI virus genomes set and make a blast database out of that.

If you're just interested in assigning taxonomic identity to your contigs, you may want to try something like MASH: http://biorxiv.org/content/early/2015/10/26/029827 https://github.com/marbl/Mash

Answer 2

[ARich]

Thanks for your quick reply. these are illumina reads 2X150. It has bacterial sequences as well. I generated contigs using spades and now would like to see the taxonomic classification only for viruses. I tried downloading all gbvrl files but i dont know how can i created single fasta file out of it. So that i can create viral DB and just classify using megan. I will try Mash for now.

Thanks

[pld]

If they're in fasta format, you can just concatenate them. I believe that makeblastdb can also read database sequences from stdin, so you can pipe it in.

You should be able to just use the RefSeq sketch that is on the Mash website.