Why some bins include only one contig?

[jiaojiao guan]

Dear developer,

Thanks very much for your excellent tool. When I used MetaBAT2 to do multi-sample binning, I found that some bins only included one contig. I downloaded the latest version yesterday(20/08/2024).

Why are there some bins that only contain a single contig? Any reasons for leaving these contigs as a bin? Why these contigs do not belong to the unbinned file? Thanks very much for your reply.

‌

Best Regards,

Jiaojiao

‌

[Rob Egan]

If there is a bin with only 1 contig, then it is a very long contig (i.e. >= --minClsSize default 200kb) without anything else large enough (i.e. >= --minSmallContig default 1000b) and similar enough to recruit to it. You might have a plasmid or virus, or a large fraction of a complete genome.

[jiaojiao guan]

I see. Thank you for your help!