Hi, good morning. I am now trying to use metatdenovo to assemble my viral sequences. I ran a test run to assemble one sample specifying --spades_flavor=metaviral. The output files are a contig.fa.gz and a scaffold.fa.gz. Now I want to bin it to MAGs. Could you suggest some further method for me to proceed?

this is concoct https://concoct.readthedocs.io/en/latest/

Thank you. I will try them out.

Viral sequences can't be binned with tools for bacteria.

ops! then what about this: https://github.com/AnantharamanLab/vRhyme?

That could be something! 🙂 Pursuing option 1, i.e. look for long contigs, might also take you quite far.

I will check both.

It would be interesting for us to see some statistics of your assembly. Can you post the content of the

.csv

file from the

TRANSRATE

process? This should be in the

results/transrate

directory but it seems we might have a small bug here since I can't find it in a test run I did. If you can't find it anywhere under

results

, see if you can find it in the

work

directory (Danilo can help).

Hi, I found a directory named

spades_transrate

in

work

. Not sure if that's what you asked for, here's what's inside.

contig_name,length,prop_gc,orf_length
NODE_1,142902,0.360786,832
NODE_2,81378,0.384084,834

Is that the only file? These are statistics for individual contigs (are there only 2?!). I'm interested in a file that contains overall statistics like lengths, N50 etc. Might be in the parent directory to the one you mention.

That's the only one file in the whole parent directory. And it seems correct since my viral metagenome is just a mix of two isolates.

I see, we thought it was a metavirome! 🙂 All good then, you have two long contigs, one for each isolate. No binning or anything like that needed. You can proceed with annotation with #C05E9C2B2BG or any other tool you prefer.

That's good news. And I actually found the binning tool

vRhyme

integrated in #C05E9C2B2BG . Good to know for future usage.