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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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Bin merging example set #26

Open mkellom opened 2 years ago

mkellom commented 2 years ago

Do you have a set of sample bins where you know merging should occur?

I have been running the bwa bin merging steps on some bin folders and so far no merging has occurred. So I'm curious if you have a working positive control sample set that you recommend.

Thank you

mkellom commented 2 years ago

Also, do you know if using the actual contigs for creating a sorted alignment yields much better results than using pseudo contigs from concatenated bins? Or are bins merged just as well either way?

openpaul commented 2 years ago

Sorry I was away for a while. I dont have a benchmark dataset that I can share at the moment. You can force it by simply splitting a single eukaryotic MAG into two bins. But of course this would be an artificially created dataset.

I hope I can share datasets soon (Send me an email and I can share some accessions).

I am also working on a test case for the tutorial, but want to keep it simple, and thats hard to create.

openpaul commented 2 years ago

Regarding the alignments: In our pipeline we use concatenated bins but I dont see any issues using the assembly or the concatenated bins. Usually they are very similar.

If contigs are in multiple bins this whole process needs to be re-evaluated though, as currently the scripts assume a contig is in a single bin.

I am not sure if that answers the question?

mkellom commented 2 years ago

Yes, it does. Thank you!