Tools for metagenomic binning for viruses?

Question

[jaydu]

Hi there!

I wonder if there is a tool which performs binning of reads or contigs from RNAseq of whole organisms (arthropods) to identify viruses. For now I blast all contigs and extract the taxids of the best hits and manually extract the ones for viruses. This seems very inefficient! :)

Thanks for pointing me in the right direction...

Answer 1

[Mensur Dlakic]

There are many tools for contig binning, and I will list some of them below in my order of preference. Not only are they more efficient in assigning contigs into bins, but they are also more objective as the underlying nucleotide composition is always there even when BLAST hits are missing or ambiguous.

• https://github.com/BinPro/CONCOCT
• https://bitbucket.org/berkeleylab/metabat/src/master/
• https://github.com/tetramerFreqs/Binning
• https://github.com/claczny/VizBin

One can combine multiple binning results by finding a consensus:

• https://github.com/songweizhi/Binning_refiner

There is nothing special that needs to be done for viruses. If their nucleotide composition is different from a host - and it usually is - they will end up in separate bins that are usually smaller and placed on the periphery of the embedding plot.