Hi
Does anyone know the genome size of each bin?
I binning contigs and get bins, so each bins can regard as one genome, but how i can know the genome size.
My thought is in each bins it has many contigs, and I cluster them with cover 95% to get non-redundant contigs set, and then adding all length of contigs in the non-redundant contigs set, and this value is the genome size of each bin.
Is this right?
1 answer
The answer is that you can't be sure of the genome size with certainty. But yes, the sum of contigs is indicative of genome size, especially if you confirm that a bin has a genome that is mostly complete and not terribly contaminated. A tool like CheckM can provide that information.
I don't think you need to remove the redundancy in your bins. I recommend higher identity threshold like 99% if you still want to do it.
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sorry to tell , but way too little info in your post to get meaningful (if any at all) replies on it.
what kind of bins are you talking about? related to a tool or software you are using?
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You should not remove redundant contigs. By doing so, you could falsify the
strain heterogeneityindex from CheckM.