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soedinglab / metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
GNU General Public License v3.0
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Your opinion on Miniprot #81

Open shelkmike opened 1 year ago

shelkmike commented 1 year ago

In the preprint about Miniprot (https://arxiv.org/abs/2210.08052) the author claims that it is usually more accurate than MetaEuk. Do you agree?

hyphaltip commented 1 year ago

miniprot is an aligner while metaeuk is a gene predictor so I don't think these are necessarily head to head comparison

shelkmike commented 1 year ago

Miniprot is integrated into Compleasm (previously known as MiniBUSCO) and it demonstrates a better capability of BUSCO genes' prediction than BUSCO itself (which uses MetaEuk) https://www.biorxiv.org/content/10.1101/2023.06.03.543588v1 .

martin-steinegger commented 1 year ago

@shelkmike what do you try todo? Knowing your use-case would help us to guide what tool to use.

shelkmike commented 1 year ago

@martin-steinegger The main reason I'm asking is that I'm trying to understand whether Compleasm should be preferred to BUSCO. Their main difference is that Compleasm uses Miniprot while BUSCO uses MetaEuk. If authors of MetaEuk agree that Miniprot is more accurate, this would be a good argument to use Compleasm.