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Guillaume Holley

@guillaumeolesan.bsky.social
374 followers 178 following 24 posts

Principal Scientist @ deCODE Genetics. Working on pangenomes | PGx/CMRG genes | long reads. "There is no peace amongst the stars, for in the grim of darkness of the far future, there is only war" - W40K Views and opinions are my own.

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Reposted by Guillaume Holley
Science Magazine @science.org · 04/10/2026
A species of lungfish found in South America has claimed the title of the animal with the biggest genome sequenced so far. Learn more on #WorldAnimalDay: scim.ag/46OMl6v
This odd fish has 30 times as much DNA as humans—a new record for animals
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Reposted by Guillaume Holley
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 20/09/2026
Somatic haplotype reconstruction and variant recalibration from tumor-only long-read sequencing www.biorxiv.org/content/10.64898/20…
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Guillaume Holley @guillaumeolesan.bsky.social · 20/08/2026
I am delighted to present with @hannespetur.bsky.social our new study on the Icelandic pangenome reference HPRC-ICE. This work goes all the way from pangenome construction to disease association! (1/7) www.nature.com/articles/s41...
nature.com
An Icelandic pangenome reference - Nature
Newly developed methods enable construction of Icelandic haplotypes and mapping of population-scale short reads to a pangenome by reducing reference bias and improving discovery in low-mappability reg...
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Reposted by Guillaume Holley
Mao-Jan Lin @maojanlin.bsky.social · 03/08/2026
1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps by leveraging linkage disequilibrium and sequence identity between contigs and reference haplotypes Code: github.com/maojanlin/Im...
biorxiv.org
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies
With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...
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Reposted by Guillaume Holley
Brynja Sigurpálsdóttir @brynjad.bsky.social · 30/07/2026
Excited to share our new paper in Nature Communications! rdcu.be/fwOV9 We used @nanoporetech.com to sequence 7,284 individuals and measured DNA methylation at ~18 million high-quality CpG units across the genome (1/5)
rdcu.be
Nanopore sequencing identifies parent-of-origin specific age-associated methylation changes at imprinted loci in the human genome
Nature Communications - DNA methylation changes with age, but parent-of-origin effects remain poorly characterised. Here, the authors use nanopore sequencing to map age-associated methylation...
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Reposted by Guillaume Holley
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/07/2026
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies www.biorxiv.org/content/10.64898/20…
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Aaron Sojourner @aaronsojourner.org · 25/07/2026
Admirable clarity @science.org
The Trump administration hates academic science funding, full stop. They hate where that money goes, and they hate who it goes to. They want to keep all that money for themselves, to hand out to favored cronies who can help them get elected and to steer yet more money and more power back into their hands.

That’s it. That’s the story
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/07/2026
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation www.biorxiv.org/content/10.64898/20…
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Reposted by Guillaume Holley
Vikram Shivakumar @vikramshivakumar.bsky.social · 15/07/2026
1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools
biorxiv.org
Navigating the pangenome coordinate system with Shredtools
Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...
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Reposted by Guillaume Holley
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 09/07/2026
Lossless compression of k-mer matrices enabling random row access www.biorxiv.org/content/10.64898/20…
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Reposted by Guillaume Holley
Shuangjia Lu @lushjia.bsky.social · 07/07/2026
🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...
doi.org
Pangenome-based human genome analysis improves trait association and genomic prediction
The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...
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Reposted by Guillaume Holley
Adam Phillippy @aphillippy.bsky.social · 29/06/2026
Complete diploid genomes anchored to the pangenome and interpreted with the help of AI models. Endorsed! We are very actively building towards this future for medical genetics 🔮
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Zamin Iqbal @zaminiqbal.bsky.social · 25/06/2026
Honoured to be awarded the Mary Lyon medal by the Genetics Society today, here in Edinburgh. V grateful to mentors and all my previous group members and colleagues. Medal is an X chromosome!!
Gold/bronze coloured medal, with depicted X chromosome Second side of medal says "Mary Lyon Medal" awarded to Prof Zam Iqbal. By the Genetics Society
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Reposted by Guillaume Holley
Ben Langmead @benlangmead.bsky.social · 22/06/2026
Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)
academic.oup.com
Validate User
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Reposted by Guillaume Holley
Heng Li @lh3lh3.bsky.social · 16/06/2026
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
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Reposted by Guillaume Holley
Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/06/2026
Happy to see that K2Rmini was recommended today by PCI Mathematical & Computational Biology. "quickly evaluate whether an arbitrary sequence has a number of k-mer [of interest] matches above or below a threshold." by @imartayan.bsky.social and colleagues: www.biorxiv.org/content/10.1...
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Reposted by Guillaume Holley
Ryan Wick @rrwick.bsky.social · 11/06/2026
New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...
rrwick.github.io
Dorado v2.0.0: no more sup?
a blog for miscellaneous bioinformatics stuff
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Adam Phillippy @aphillippy.bsky.social · 08/06/2026
T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 29/05/2026
1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster
github.com
GitHub - pierrepeterlongo/logan_blaster: Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Lo...
Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Logan-Search results) run a local blast ...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/05/2026
Fast Set Operations for Compact k-mer Sets www.biorxiv.org/content/10.64898/20…
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Genome in a Bottle Consortium @genomeinabottle.bsky.social · 06/05/2026
Excited to announce we’ve constructed a complete, haplotype-resolved assembly of a human pancreatic cancer genome. By comparing tumor cell line and normal tissue assemblies directly, we developed phased somatic benchmarks. Thanks to many in GIAB! www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Guillaume Holley
Heng Li @lh3lh3.bsky.social · 30/03/2026
LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel. Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL
rdcu.be
SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads
Nature Methods - In this study, long-read RNA sequencing achieves accurate single-nucleotide polymorphism calling, haplotype phasing and allele-specific expression analysis.
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Reposted by Guillaume Holley
Sam Horsfield @samuelhorsfield.bsky.social · 30/03/2026
ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on... github.com/bacpop/ggCal...
github.com
GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
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Reposted by Guillaume Holley
Adam Phillippy @aphillippy.bsky.social · 23/03/2026
Recently amplified gene arrays are a super interesting phenomenon, but many still resist our attempts to assemble them. @dantipov.bsky.social has developed a new method (Trivial Tangle Traverser) that resolves assembly graph tangles caused by such sequences (1/4) www.biorxiv.org/content/10.6...
biorxiv.org
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Heng Li @lh3lh3.bsky.social · 23/03/2026
Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.
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Reposted by Guillaume Holley
Lior Pachter @lpachter.bsky.social · 06/03/2026
kallisto sped up RNA-seq quantification by 50x. Now another 50x speedup... quantify hundreds of millions of reads in a few seconds. This seems too good to be true. But it's true! Incredible accomplishment by @pmelsted.bsky.social.
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Andrew Carroll @acarroll.bsky.social · 07/03/2026
Release of DeepVariant v1.10 Phased VCF output for long-reads Accuracy improvements for multi-allelic variants Pangenome accuracy improvements (18% fewer errors) Most technologies ~10% faster RNA-seq is a full supported mode DeepSomatic is 12-40% faster github.com/google/deepv...
github.com
Release DeepVariant 1.10.0 · google/deepvariant
DeepVariant: Continuous phasing: Long-read variant calls (PacBio and ONT) are now natively phased and phased output is generated for both vcf and gvcf formats. Fuzzy channels: Added “fuzzy channel...
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Reposted by Guillaume Holley
Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Reposted by Guillaume Holley
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 03/03/2026
Minimum Unique Substrings as a Context-Aware k-mer Alternative for Genomic Sequence Analysis www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 03/03/2026
A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes www.biorxiv.org/content/10.64898/20…
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Reposted by Guillaume Holley
Wei Shen 沈 伟 @shenwei356.bsky.social · 27/02/2026
Can't wait to release a 10-year-old birthday version for SeqKit! - 10 years - 2 papers, 3500 citations - 20 contributors - 40 subcommands - 880 commits - 500 issues - 685.5K Bioconda total downloads Thank you all, dear contributors and users! I'll keep maintaining it. github.com/shenwei356/s...
github.com
Release SeqKit v2.13.0 (10-year-old birthday version) · shenwei356/seqkit
Changelog SeqKit is 10 years old! SeqKit v2.13.0 - 2026-02-28 seqkit: add support for reading and writing LZ4 compression format. new command: seqkit sample2: improved seqkit sample by @stahiga....
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Zamin Iqbal @zaminiqbal.bsky.social · 26/02/2026
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...
allthebacteria.readthedocs.io
Overview — AllTheBacteria documentation
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Antoine Limasset @npmalfoy.bsky.social · 04/02/2026
Preprint alert! arxiv.org/abs/2602.03525 TLDR: ZOR filters are STATIC filters with false positives. -Almost memory optimal: <1% overhead over the theoretical lower bound (!!!) -Fast queries: ~100 ns -Construction cannot fail A thread:
arxiv.org
ZOR filters: fast and smaller than fuse filters
Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...
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arXiv cs.DM Discrete Mathematics @csdm-bot.bsky.social · 04/02/2026
Florian Ingels, Antoine Limasset, Camille Marchet, Mika\"el Salson: Vigemers: on the number of $k$-mers sharing the same XOR-based minimizer arxiv.org/abs/2602.03337 arxiv.org/pdf/2602.03337 arxiv.org/html/2602.03337
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Zamin Iqbal @zaminiqbal.bsky.social · 30/01/2026
"trio-based long-read phasing method that integrates multi-k-mer parent-specific markers with an alignment-free k-mer lookup engine and a random forest classifier to assign long reads to maternal, paternal, or unknown haplotypes prior to de novo assembly"
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 23/10/2025
Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
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Mohsen Zakeri @mohsenzakeri.bsky.social · 21/10/2025
1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...
github.com
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
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Guillaume Holley @guillaumeolesan.bsky.social · 10/10/2025
www.nature.com/articles/s41...
nature.com
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
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Matt Holt @holtjma.bsky.social · 06/10/2025
I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months! Aardvark: Sifting through differences in a mound of variants GitHub: github.com/PacificBiosc... Some highlights in this thread: 1/N
github.com
GitHub - PacificBiosciences/aardvark: A tool for sniffing out the differences in vari-Ants
A tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark
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Xian Chang @xian-chang.bsky.social · 02/10/2025
🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
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Adam Phillippy @aphillippy.bsky.social · 22/09/2025
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
biorxiv.org
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
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Javier Santoyo @jsantoyo.bsky.social · 23/09/2025
colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs. #SomaticStructuralVariants #SV #CoassemblyGraphs #Bioinformatics #Genomics #GenomicsProteomicsBioinformatics academic.oup.com/gpb/advance-...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 19/06/2025
In silico discovery of pathogenic PD-L1 nsSNVs with altered glycosylation and immunotherapy binding www.biorxiv.org/content/10.1101/202…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/06/2025
REINDEER2: practical abundance index at scale www.biorxiv.org/content/10.1101/202…
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Adam Phillippy @aphillippy.bsky.social · 17/06/2025
Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/06/2025
Pangenome-aware DeepVariant www.biorxiv.org/content/10.1101/202…
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 27/05/2025
📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8
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Tommi Mäklin @themaklin.bsky.social · 26/05/2025
New preprint: we used k-mer matching with suffix match length information to create an assembly-to-assembly alignment algorithm + software, kbo. We wanted to create a reference-based aligner and variant caller that scales to at least 10-100k bacterial queries. www.biorxiv.org/content/10.1...
biorxiv.org
Sequence alignment with k-bounded matching statistics
Finding high-quality local alignments between a query sequence and sequences contained in a large genomic database is a fundamental problem in computational genomics, at the core of thousands of biolo...
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Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025
Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...
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Human Pangenome Reference Consortium @humanpangenome.bsky.social · 12/05/2025
📢 HPRC Release 2 is here! Now with phased genomes from 200+ individuals, a 5x increase from Release 1. Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️: humanpangenome.org/hprc-data-re...
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