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:

Florian Ingels, Antoine Limasset, Camille Marchet, Mika\"el Salson: Vigemers: on the number of $k$-mers sharing the same XOR-based minimizer https://arxiv.org/abs/2602.03337 https://arxiv.org/pdf/2602.03337 https://arxiv.org/html/2602.03337

"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"

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.

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...

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

🦒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

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]

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-...

In silico discovery of pathogenic PD-L1 nsSNVs with altered glycosylation and immunotherapy binding https://www.biorxiv.org/content/10.1101/2025.06.17.660108v1

REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1

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...

Pangenome-aware DeepVariant https://www.biorxiv.org/content/10.1101/2025.06.05.657102v1

📜 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

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...

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...

📢 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...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Not only is this seriously elegant science from @gregfindlay.bsky.social, @nickywhiffin.bsky.social and friends - using saturation editing to define variant impact in RNU4-2 - it also defines *another* new syndrome associated with this fascinating non-coding RNA gene.

Finally got around to fixing the main limitation of the current vcfdist release: exploding memory usage and runtime in regions with high-density variants. A new `--max-supercluster-size` parameter limits this. Release v2.6.0 is out on [Github](github.com/timd1/vcfdist), DockerHub, and bioconda!

A milestone for our lab! Here's a full access link: rdcu.be/egmYb

The Genetics research community has a problem. Most recent articles do not consider #splicing/isoforms. Here, we analyze how important this opportunity gap is - and spoiler warning - we find it is essential for both analysis of common and rare variants More info👇 www.medrxiv.org/content/10.1...

Congratulations to @imartayan.bsky.social and @curiouscoding.nl whose paper on fast minimizer computation with simd has been accepted to SEA 2025 🙌🏻 www.biorxiv.org/content/10.1...

"Our results reveal substantial differences between pipelines, with many inversions either misrepresented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches."

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1 🧬🖥️🧪 https://github.com/harvardinformatics/scrub-jay-genomics

Pangenome graph augmentation from unassembled long reads https://www.biorxiv.org/content/10.1101/2025.02.07.637057v1

Our study reveals that the MLLT3 gene, crucial for maintaining the self-renewal of some bloom stem cells, also produces a truncated version of its protein via an alternative process. REINDEER was the indexing technique behind the discovery, more here: onlinelibrary.wiley.com/doi/10.1002/... 2/2

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline. #StructuralVariants #GenomeAssembly #Bioinformatics #Genomics @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

Haplotype-based Parallel PBWT for Biobank Scale Data https://www.biorxiv.org/content/10.1101/2025.02.04.636317v1

Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3 https://www.biorxiv.org/content/10.1101/2025.02.02.636161v1

Evaluation of sequencing reads at scale using rdeval https://www.biorxiv.org/content/10.1101/2025.02.01.636073v1

Complete human recombination maps www.nature.com/articles/s41... - continuation of 25 yeas of work in building recominbation maps.

Trump presidency started something like 30 seconds ago

📌 Registrations for #RECOMB2025 are now open! 📌 Visit recomb2025.com for details. The early registration deadline is March 15, 2025.

Review: Pangenome graphs and their applications in biodiversity genomics https://www.nature.com/articles/s41588-024-02029-6 (read free: https://rdcu.be/d5Bv7) 🧬🖥️🧪

Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity https://www.biorxiv.org/content/10.1101/2025.01.06.631535v1

Some good news to kickstart 2025.

Mumemto: efficient maximal matching across pangenomes https://www.biorxiv.org/content/10.1101/2025.01.05.631388v1

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

Another year in the books! 🗓️ HPRC wishes everyone a joyous start to 2025! 🎉 As we roll into a new month, in a new year, we look forward to continued collaboration, innovation, and progress in genomics research. #happynewyear

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding https://www.biorxiv.org/content/10.1101/2024.12.20.629807v1 🧬🖥️🧪 https://github.com/marbl/verkko

Although I don't disagree with the main message here, the plot twist is that "his" image on the left is photoshopped (from his own admission on Instagram) because capturing a northern light and a polar bear at the same time is "very tough"

Merry lexicographic minimiz... Christmas arxiv.org/abs/2412.17492

I recently finished painting up this homebrew Salamanders successor for a video on how light interacts with different materials. Link below and more pics in the comments! youtu.be/MDlbqIBpTCM #warhammer40k #paintingwarhammer #nerdlings

Kateryna Makova and I have a new preprint out on non-canonical DNA in human and ape T2T genomes: www.biorxiv.org/content/10.1... Collaboration with Kaivan Kamali, Francesca Chiaromonte, Eduard Kejnovsky, and Iva Kejnovska. Graphical abstract by Dani Zemba.

We're thrilled to introduce LexicMap v0.5.0🎉 It's more accurate and slightly faster! LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes! We'll provide an index for ATB on AWS later. github.com/shenwei356/L...

💡HPRC research is reaching new heights. Hifiasm (UL) combines multiple sequencing technologies for efficient, population-wide, near-telomere-to-telomere assemblies. discover the revolutionary science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157... www.biorxiv.org/content/10.1... 1/5

www.biorxiv.org/content/10.1... 🖥️🧬