iiinova — where your digital self keeps evolving

Pierre Peterlongo @pierrepeterlongo.bsky.social · 09/07/2026

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...

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 09/07/2026

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. 🧵

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 08/07/2026

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...

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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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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

🛠️ 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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 29/05/2026

📊 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.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 29/05/2026

—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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 21/11/2025

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...

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 27/05/2025

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 27/05/2025

🔍 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

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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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Pierre Peterlongo @pierrepeterlongo.bsky.social · 20/03/2025

Note that the "conservative update" is also something we implemented (without describing it) in fimpera github.com/lrobidou/fim...

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 18/03/2025

Results: slightly longer insertion time, but 2 to 3 times lower abundance overestimations.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 18/03/2025

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

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 18/03/2025

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... 🧪🧬🖥️

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 12/12/2024

🚨🚨🚨 We are hiring 🚨🚨🚨 After the creation of logan-search (see: bsky.app/profile/pier...) we propose a 2-years engineer position for continuing the development and optimizations. With @rayanchikhi.bsky.social and @tlemane.bsky.social Details + applications: recrutement.inria.fr/public/class...

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 04/12/2024

Amazing ideas here www.biorxiv.org/content/bior... from @yoann.bsky.social and collaborators. Reorganize minimizers to allow kmers dichotomic search. That's brilliant. #bioinformatics 🧬🖥️

Toy example of the AAAAAAA bucket associated to four super-k-mer turned into their interleaved representation.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024

🔬 We anticipate this tool will revolutionize the accessibility of public genomics data. Our hope is to empower new discoveries by the community 💖 Developed w/ @TeoLemane, & collabs @RayanChikhi, @RNA_Life, Alex Morales, and Luke Pereira

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024

🧪 Logan Search returns a list of SRA accessions, not alignments. To bring you closer to the data we’ve also created a microservice to instantly retrieve Logan contigs matching your search.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024

📊 The output datasets are easily visualized with custom plots in Logan Search, which accesses a harmonized set of query and SRA meta-data including sequencing technology, type of molecule, geographic distribution, and sample origins. Learn more about your sequence.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024

Logan Search transforms your query🧬 to its k-mers🔢 (k=31), and in the time it takes to brew a coffee, it will retrieve every dataset containing your k-mers. It’s the only service working at this scale.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience

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