Is it necessary to conduct binning after assembly with HiFi reads to get MAGs?
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Hello, xfengnefx!
With NGS shotgun reads, to get MAGs we usually assemble pair-end reads into contigs, and then recover MAGs through binning.
What I want to ask is that for HiFi reads, in order to get MAGs with higher quality whether it is necessary to conduct binning after we get contigs using hifiasm-meta?
Thanks for your helping.
@ye00ye (not sure if you can get notifications on closed issue so I'm pinging)
Binning is still useful, but it looks less efficient than what you get in NGS. Usually a good bin will only contain 1-3 long contigs for HiFi assemblies (tried metabat2 and vamb). Bins with more contigs are likely to be contaminated. I'm not sure why. I haven't tried the newer ones.
The current HEAD has a rescue heuristic based on contig graph topology. Checkout the prefix.rescue.fa file if you ran it. Each fasta entry in this file is guessed to be a circular(ized) MAG.
This is error-prone and you definitely need to checkM these rescues.
We are preparing a manuscript on this and subsequent evaluation methods. The preprint probably will come out a couple weeks from now. I'll push some changes by then, too.