Pierre Peterlongo

4 Sept 2025

❗ I clearly consider this result as THE most important result achieved over this last decade for exploiting and democratizing genomic data. I think there will be a "before" and an "after" logan and logan-search github.com/IndexThePlan... logan-search.org Have a look at this thread

Rayan Chikhi@rayanchikhi.bsky.social

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

1/ 🧬 & 🖥️ New tool: kmhelpers — a Python toolkit dedicated to kmindex, automating the building, updating & querying of large-scale k-mer genomic indexes. Turning raw sequencing samples into a fast, size-optimized search engine — without needing to be a Bloom-filter expert. 🧵

6/ kmhelpers wraps kmindex (Lemane et al.) and kmtricks, is Python ≥3.8, Conda-installable, with a CLI (Click) and matching Python API. GPLv3, open source. Code: github.com/sebllns/kmhe... Docs: sebllns.github.io/kmhelpers/

github.comgithub.com

7/ Work by Sébastien Bellenous, Kamil S. Jaron @kamilsjaron.bsky.social (Genscale, Univ. Rennes / Inria / CNRS / IRISA + Wellcome Sanger Institute). Paper (JOSS submission draft): github.com/sebllns/kmhe...

4/ It also handles indexes grow. As new samples arrive constantly kmhelpers supports incremental updates — and `manage` federates several independently built indexes into one logical, queryable resource.

5/ Real-world use: • Tree of Life @ Wellcome Sanger Institute: 7,394 samples indexed, now powering sample-swap detection across the Darwin Tree of Life project. • Logan-Search (~50 petabases from SRA): next update will use kmhelpers to re-optimize the index.

2/ The problem: k-mer indexes (à la BIGSI, COBS, kmindex...) let you search for a sequence across thousands of samples using Bloom filters. But building an *efficient* one means hand-tuning BF sizes, memory, data distribution & sub-index grouping — for every sample, every time.

3/ kmhelpers automates the whole chain: list → profile → compose → plan → apply → query It picks BF sizes and sample-to-sub-index assignments that minimize total index size under a false-positive-rate constraint, estimates disk/RAM upfront, and generates ready-to-run pipelines.

github.comRelease Minibwa-0.3 (r391) · lh3/minibwaNotable changes: New feature: added the mem subcommand to mimic the bwa-mem command-line interface (CLI). Most input/output options and commonly used options are retained; unsupported or incompat...

8 July

Might be useful. Here is a short blog entry describing a tool that annotates a PDF using a text file. I couldn't find anything that simply does this single task, so I created this. Blog post: pierrepeterlongo.github.io Git repo: github.com/pierrepeterl...

Pierre Peterlongo reposted

Heng Li

@lh3lh3.bsky.social

28 June

minibwa v0.3 released with a few minor bug fixes and two missing bwa-mem features (XA tag for secondary hits and option -H to inject header lines). Also added the "mem" subcommand to mimic "bwa mem" CLI to some extent. github.com/lh3/minibwa/...

Pierre Peterlongo reposted

Ben Langmead

@benlangmead.bsky.social

22 June

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.comValidate User

nature.comOrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature MethodsThe updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

11 June

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...

Pierre Peterlongo reposted

Federico Lopez

@flopezos.bsky.social

9 June

📄 OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability 🧬🖥️ ⬇️ www.nature.com/articles/s41...

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

🛠️ logan_blaster: a command-line tool that automates the alignment step locally, with no timeout constraints. github.com/pierrepeterl... conda install -c bioconda logan_blaster

rayanchikhi.bsky.socialRayan Chikhi (@rayanchikhi.bsky.social)

🙏 Thanks: rayanchikhi.bsky.social tlemane.bsky.social rnalab.bsky.socialand the whole logan team! Paper: www.biorxiv.org/content/10.1...

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

9/12 🎬 A 5-min tutorial covers both basic usage and deeper features for new and returning users. See docs.logan-search.org

🔍 Raising your attention to the BLAST-like alignment tab: you can perform proper alignment of the query against assembled contigs or unitigs directly in the browser. It is limited to one sample at a time and may timeout on large inputs. Which is why we built the next tool.

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

7/12 📄 When publicly available, the scientific paper(s) associated with matched samples are provided.

8/12 🤖 The AI summary of query results has been improved and now provides much more information.

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

5/12 🧬 Matches to RefSeq reference genomes are now included in results.

6/12 📊 Results now come with an e-value, a p-value, and an ANI estimation.

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

3/12 ⚡ New fast mode: queries 99.5% of non-viral SRA samples, around 2x faster.

4/12 🎨 The interface got a refresh: new query history, email input is optional.

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

2/12 📏 Query length limit raised: 1000 → 2500 bp. One of the most-requested changes.

github.comGitHub - 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 ...

1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster

📊 Synthesis files show per-position query coverage using letter codes (a–z, then Z for 26+ contigs) — a compact view of how contigs pile up along your query sequence.

tlemane.bsky.socialTéo Lemane (@tlemane.bsky.social)

—8/8 🙏 Thanks to tlemane.bsky.social for key contributions, and the whole logan team!

1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster

—5/8 🎛️ Key options: Using a logan-search session ID (received by email) -s Logan-search session ID Or for any sequence with any accessions list: -q query FASTA -a accessions file General options: -u align against unitigs instead of contigs -l limit number of accessions processed

📁 Output structure: alignments/ — BLAST results per sample logan_data/ — downloaded contigs or unitigs and recruited sequences failed_accessions.txt — samples that couldn’t be downloaded

1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster

—3/8 ⚙️ Under the hood, three steps per accession: Download Logan contigs or unitigs Recruit contigs or unitigs sharing k-mers with your query (uses github.com/pierrepeterlongo/back_to_sequences) Run local BLAST between query and recruited contigs or unitigs

—4/8 📦 Install: conda install -c conda-forge -c bioconda logan_blaster

1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster

🔗 It picks up where the Logan-search blast-like browser tab leaves off. Two modes: provide a Logan-search session ID directly or bring your own query FASTA + accessions list

Pierre Peterlongo reposted

Bioinformatics Advances

@bioinfoadv.bsky.social

7 May

🔍 New paper in Bioinformatics Advances: "Kaminari: A frugal colored index for approximate k-mer queries" Read it here: https://doi.org/10.1093/bioadv/vbag120 Authors include: @yhhshb.bsky.social, @yoann.bsky.social, @robp.bsky.social, @pierrepeterlongo.bsky.social, @jermp.bsky.social

nature.comEfficient and accurate search in petabase-scale sequence repositories - NatureMetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

21 Nov 2025

Good Friday Evening news: we updated back_to_sequences (find the origin of kmers) - Faster - Can consider multiline fasta files - Much easier installation: see github.com/pierrepeterl...

Pierre Peterlongo reposted

Rob Patro

@robp.bsky.social

9 Oct 2025

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

Pierre Peterlongo reposted

Jim Shaw

@jimshaw.bsky.social

7 Sept 2025

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

📜 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

🌊 On metagenomic data, other tools such as kmindex are good alternatives. At the same time, Kaminari consistently ranks as one of the fastest tools across all data types, generating the smallest indexes (or the lower FPR). 7/8

🤝 Amazing collaboration with @jermp.bsky.social, @yhhshb.bsky.social, @robp.bsky.social, Victor Levallois, and Bertrand Le Gal, and the help of ‪@yoann.bsky.social‬. 8/8

📊 Experimental results show Kaminari's superiority in index size and query performance across various genomic datasets. 5/8

💾 For fixed False Positive rates, it uses up to 37x less space than COBS while being an order of magnitude faster to build and query. 6/8

github.comGitHub - yhhshb/kaminari: 雷 - kaminari (thunder/lightning)雷 - kaminari (thunder/lightning). Contribute to yhhshb/kaminari development by creating an account on GitHub.

💻 We implemented Kaminari in C++17, available under the MIT license at github.com/yhhshb/kaminari. Additional results and reproducibility info at github.com/vicLeva/benchmarks_kaminari. 3/8

🧬 Kaminari's design leverages properties of k-mer minimizers for compact space and fast query time, as inspired by the techniques proposed in Fulgor. 4/8

🔍 Key findings include: - Use of minimizers and integer compression for indexing. - Lower memory footprint and faster query times. - Minimal impact of false positives on result ranking, using the Rank-Biased Overlap (RBO) metric. 2/8

18 Mar 2025

Maybe the simplest idea to decrease overestimations of a counting bloom filter. A trivial observation + 10 lines of code. I'm surprised it has not been described before. Please comment if this is not the case. Blog post here: pierrepeterlongo.github.io/2025/03/17/m... 🧪🧬🖥️

18 Mar 2025

In two words: increase only minimal stored values of a cBF when adding elements to this filter.