Hifiasm published in Nature Methods. 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 Haoyu Cheng gconcepcion.bsky.social Xiaowen Feng Haowen Zhang

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

Latest from Haoyu Cheng, Heng Li 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.

The previous hifiasm paper described haplotype-resolved assembly with trio data. In this new paper, Haoyu Cheng 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.

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…

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 Heng Li. Source code: github.com/chhylp123/hifi…

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

My new lab at Yale Biomedical Informatics & Data Science 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 Heng Li and collaborators for their incredible support!

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…

The latest hifiasm can directly assemble standard Oxford 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.