Haoyu Cheng
@ChengChhy
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.
Exciting news! The latest hifiasm release from @ChengChhy and @lh3lh3 adds beta support for @nanopore simplex R10 reads. Initial results look very promising. 🚀 Check it out: github.com/chhylp123/hifi…"
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! github.com/chhylp123/hifi…
My new lab at @YaleBIDS is looking for a couple of postdocs, students and RAs in bioinformatics, genomics, machine learning and related fields (postdocs.yale.edu/postdoctoral-a…). Heartfelt thanks to my mentor @lh3lh3 and collaborators for their incredible support!
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 arxiv.org/abs/2409.00613
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: github.com/chhylp123/hifi…
Today is the big day! The #T2T consortium is claiming victory and announcing that we have finally uncovered every last bit of the human genome! The papers are out today 🥳🧬 science.org/toc/science/37…
The previous hifiasm paper described haplotype-resolved assembly with trio data. In this new paper, @ChengChhy achieves chromosome-long phased assembly without parents. Tested for human and non-human species. A single executable and one command line for the entire process.
The latest hifiasm for single-sample haplotype-resolved assemblies from our lab @lh3lh3 is published on Nature Biotechnology @NatureBiotech. Journal paper: nature.com/articles/s4158… and read-only link: rdcu.be/cJM9E.
Latest from @ChengChhy, @lh3lh3 and collaborators: Haplotype-resolved genome assemblies produced by the new #hifiasm algorithm could accurately reveal complex genetic variations in #cancer genomes. Further development may lead to high-quality cancer #genome assemblies.
Haplotype-resolved assembly of diploid genomes without parental data go.nature.com/3Ni40ZE
Yet another genome assembler, this time it is written in Rust. Peregrine-2021: A faster and minimum genome assembler for long-reads with good enough accuracy github.com/cschin/peregri… #genomics #bioinformatics #rustlang
Hifiasm published in @naturemethods. Preprint: arxiv.org/abs/2008.01237 Source code: github.com/chhylp123/hifi… Assemblies: zenodo.org/record/4393631 & zenodo.org/record/4393750 Journal paper: nature.com/articles/s4159… Fine work by @ChengChhy @phototrophic @0xfxfxf @haowen_zhang