Haoyu Cheng

[Haoyu Cheng @ChengChhy]

Joint work with @lh3lh3, @peter_j_park, and the ONT team @vellamike.

[Haoyu Cheng @ChengChhy]

New preprint on hifiasm (ONT)! We can now achieve near T2T human genome assembly using only ONT Simplex reads—in just half a day, with or without ultra-long sequencing.

https://t.co/0tGqDGVn55

[Mike Vella @vellamike]

Telomere-to-telomere de novo assembly from standard ONT reads (LSK114, Simplex).

A really exciting advance—makes high-quality assembly practical for population-scale sequencing!

Preprint from @ChengChhy, @lh3lh3 and colleagues

https://t.co/VpQMC0DfLA

[Haoyu Cheng @ChengChhy]

@XLR @lh3lh3 @vellamike @nanopore The new version of hifiasm performs phasing, improved full-length base-level alignment rather than window-based alignment, and considers base quality.

[Heng Li @lh3lh3]

The latest hifiasm can directly assemble standard @nanopore simplex R10 reads, without HERRO correction or other preprocessing, to phased contigs of contiguity comparable to HiFi assembly. Like before, you can further add ultra-long, Hi-C or trio data for better assembly.

[Haoyu Cheng @ChengChhy]

@XLR @vellamike @lh3lh3 @nanopore It need fastq files but no other requirements.

[Haoyu Cheng @ChengChhy]

@mprous1 Then I have no idea. Probably just give it a try. Hifiasm won't take too much time.

[Haoyu Cheng @ChengChhy]

Hifiasm 0.21.0 has been released. It now has a beta module for direct assembly of ONT R10 simplex reads. Initial tests with regular simplex reads show very promising results! https://t.co/4mmPylKusz

[Haoyu Cheng @ChengChhy]

@mprous1 We tested several datasets with about 30kb N50, and hifiasm worked well.

[Haoyu Cheng @ChengChhy]

My new lab at @YaleBIDS is looking for a couple of postdocs, students and RAs in bioinformatics, genomics, machine learning and related fields (https://t.co/ZH5YZUfQ8R). Heartfelt thanks to my mentor @lh3lh3 and collaborators for their incredible support!

[Heng Li @lh3lh3]

Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB https://t.co/DiRwZNHVVa

[Haoyu Cheng @ChengChhy]

@basti_beier @HumanPangenome Oh yes, that is typo which should be fixed… Thanks for pointing that!

[Haoyu Cheng @ChengChhy]

Excited to share our new t2t assembly algorithm for diploid and polyploid genomes! Using 132 assembled haplotypes from the @HumanPangenome , we show that our approach is cost-efficient, robust, and could achieve t2t assemblies without high coverage reads https://t.co/CCvKmsA2se

[Haoyu Cheng @ChengChhy]

@basti_beier @HumanPangenome We actually used the UL reads >=50kb/100kb for the assembly. There are very small fraction of UL reads that could be longer than 500kb/1Mb.

[Haoyu Cheng @ChengChhy]

Many thanks to those who made this work possible! @asri_mobin Julian Lucas @sergekoren @lh3lh3

[Haoyu Cheng @ChengChhy]

@erikgarrison @XLR @nomad421 @lh3lh3 I checked the conda recipes: https://t.co/3O9BmbU36e, but seems there is nothing to set

[Haoyu Cheng @ChengChhy]

@jpelbers @lh3lh3 We would be happy to have a try if there is UL data for the metagenome, but sounds like it is not easy to produce UL...

[Haoyu Cheng @ChengChhy]

New hifiasm with the ultra-long integration is released! We tested it with four diploid human samples and got many T2T chromosomes. Any feedback will be much-appreciated @lh3lh3. Source code: https://t.co/63ujHGwfmp

[Haoyu Cheng @ChengChhy]

@subgenomes @lh3lh3 @PacBio @nanopore It is compatible with the old bin files, but still would be better to rerun the whole workflow from the raw reads. We would also be interested in if it could work for the polyploid genome (although it might have some parameters to be tuned).

[Haoyu Cheng @ChengChhy]

@iskander @lh3lh3 @PacBio @nanopore Yes, it is similar to the error correction in theory.

[Haoyu Cheng @ChengChhy]

@jpelbers @lh3lh3 Not sure if the ultra-long sequencing could work for the metagenome sequencing…