Heng Li
Heng Li
You can't reliably evaluate phasing errors without additional data types. The best you can do is to compare to HapCUT2 phasing, but without other data types, you don't really know...
The peak at depth 16 looks strange. It could be contamination. I would extract contigs with ~16X coverage and study what is happening. Alternatively, you can downsample input reads to...
@hhayleyj Some stages only use one thread.
@Brent-Saylor-Canopy Probably you won't see any difference in a Hi-C heatmap. The key question you need to ask yourself is how much phasing matters.
@pailloufat-stack does this sample have different sex chromosomes (like chrX/chrY for human males)?
This is probably not HiFi data.
Nextdenovo is known to produce smaller assemblies. It [gets](https://nextdenovo.readthedocs.io/en/latest/TEST2.html) a 2.9Gb human CHM13 assembly but the real size should be 3.05Gb. Hifiasm gets a 3.04Gb assembly instead, much closer to...
Whether this is resolvable highly depends on the length and sequence divergence of these regions. You have to analyze case by case.
I wouldn't trust genomescope. Its estimate is often inaccurate at our hand. You could try BUSCO.
You mean you got flow cytometry data? BUSCO does indicate 8.9% duplication rate. You could try purge_dups and see what you get. It helps to reduce duplication but may reduce...