Haoyu Cheng
@ChengChhy
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Joined October 2018
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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
biorxiv.org
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads...
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
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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:
https://t.co/Ktz0102BHL"
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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
Since Hifiasm-0.20.0 (r639): New Feature: Introduced a beta module for ONT assembly using ONT simplex R10 reads. To enable this feature, add the --ont option as shown below: hifiasm -t64 --ont -o...
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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!
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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
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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
arxiv.org
Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational...
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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
Integrated the new ultra-long ONT integration mode with the option --ul. Please note that this mode is not stable right now. There are several known issues to be fixed: The UL + HiC + trio might i...
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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 🥳🧬 https://t.co/m8wgy09JBs
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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: https://t.co/wW15T0a7Aa and read-only link: https://t.co/Ixd5lMNXwi.
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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.
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We also want to thank our collaborators @erichjarvis @ofedrigo @LaraUrban42 @ProfGemmell @ Klaus-Peter Koepfli for the fantastic help, and the datasets from @darwintreelife and @genomeark.
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We hope it will not only enable routine single-sample fully-phased assemblies, but also will be a better solution for complex SV calling.
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The latest hifiasm for single-sample haplotype-resolved assemblies from our lab @lh3lh3 is published on Nature Biotechnology @NatureBiotech. Journal paper: https://t.co/wW15T0a7Aa and read-only link: https://t.co/Ixd5lMNXwi.
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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 https://t.co/RZHOD3lbYW
#genomics #bioinformatics #rustlang
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We also want to thank our collaborators @erichjarvis @ofedrigo @LaraUrban42 @ProfGemmell @ Klaus-Peter Koepfli for the fantastic help to improve and validate the results.
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Only with HiFi reads, hifiasm also supports to output two highly contiguous primary assemblies, called dual assembly. We demonstrated dual assembly is more powerful than mapping-based methods in complex regions like GTF2IRD2. Assembly might be the ultimate solution to SV calling.
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Our lab @lh3lh3 develops a single-sample phased assembler combining @PacBio HiFi and Hi-C, which has been heavily tested for human and non-human samples ( https://t.co/s7zc5rbII5). We believe haplotype-resolved assembly for every diploid individual is becoming real before our eyes
arxiv.org
Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a...
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Hifiasm published in @naturemethods. Preprint: https://t.co/YunV6xk24V Source code: https://t.co/OF7MYAkStl Assemblies: https://t.co/Zo58ebve7L & https://t.co/9mrI9USJCR Journal paper: https://t.co/XmlnUHtfYz Fine work by @ChengChhy @phototrophic @0xfxfxf @haowen_zhang
github.com
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads - GitHub - chhylp123/hifiasm: Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
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