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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 with PacBio reads? #27

Open mkellom opened 2 years ago

mkellom commented 2 years ago

Do you have any recommendations for bin merging with PacBio reads? It seems that BWA can't handle the longer reads.

openpaul commented 2 years ago

Hmm, thats a good question. I have not yet worked with PacBio reads, are we talking long HiFi reads? In such a case I would imagine bin merging should not be needed as the assembly should not have been that fragmented I imagine.

Or am I trusting PacBio too much?

mkellom commented 2 years ago

Sorry for the very late reply.

I guess I don't know how fragmented PacBio assemblies will be. I'm mostly asking just to be prepared for the future, where I will potentially be trying to use EukCC on hundreds of PacBio metagenomes. It sounds like for PacBio sequencing, I could probably skip the bin merging step. Would you agree with that, in general?

Thank you for your insight! Matt

mkellom commented 2 years ago

I just noticed that two bins assembled from PacBio reads were merged into a single high-quality bin using EukCC2 and without attempting the BWA/SAM-tools preparation, which is great. But does this mean that the bin merging prep steps are unnecessary for EukCC2?

openpaul commented 2 years ago

They are optional, but not unnecessary as they will provide more confidence for you and speed up merging for large metagenomes. The merging without the read files are based on marker genes alone. But I have generally I have made good experience even without the paired read information, yes.