Using multiple bam files for viral genome binning

[mshamash]

Thank you for making this tool, it's been a great help in analyzing our Hi-C datasets.

I was wondering if there is any way we can use multiple bam files for the viral genome binning? In our case, we conducted a coassembly with MEGAHIT on multiple longitudinal samples from the same environment. I ran ViralCC using the bamfile from each sample, but with the contigs from coassembly, however the viral bins have different names which makes it difficult to dereplicate/merge bins.

[dyxstat]

Thanks for trying our method! However, currently, ViralCC does not allow viral contig binning using multiple bam files.

How about merging all bam files into one as the input? I think it does not hurt for the binning.

Best

[mshamash]

Thanks for the quick reply! That makes sense, I will give it a try and see how it goes.

Would a similar approach work for your other tool, HiCBin, as well? I can also open a new issue on that repo... I see you use coverage information (with the jgi_summarize_bam_contig_depths script) as part of the binning process, and am not sure if merging all my reads from the coassembly could skew or affect this...

Cheers.

[dyxstat]

Yes, your concerns make sense. When we designed HiCBin, we focused on contig binning using a single sample since almost all metagenomic Hi-C datasets only contained one sample at that time. My gut feeling is that HiCBin cannot be applied to multiple samples though you can still have a try.

You might also try bin3C instead which does not require the coverage information for binning.

Best