Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity

2024/07/31 by Rayan Chikhi, Téo Lemane, Raphaël Loll-Krippleber +28 · 2 voices · 73 citations
Biochemistry, Genetics and Molecular Biology · #Biology #Cartography #Cloud computing #Computational biology #Computer science #DNA #DNA sequencing #Data mining #Data science #Database #Dissemination #Gene #Gene expression and cancer classification #Genetics #Genome #Genomics and Phylogenetic Studies #Geography #Massive parallel sequencing #RNA and protein synthesis mechanisms #Scale (ratio) #Sequence (biology) #Sequence assembly #Snapshot (computer storage)

paper · pdf · doi:10.1101/2024.07.30.605881

published in bioRxiv (Cold Spring Harbor Laboratory) (Cold Spring Harbor Laboratory)

openalex publication_date 2024/07/31 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

Abstract The breadth of life’s diversity is unfathomable, but public nucleic acid sequencing data offers a window into the dispersion and evolution of genetic diversity across Earth. However the rapid growth and accumulation of sequence data have outpaced efficient analysis capabilities. The largest collection of freely available sequencing data is the Sequence Read Archive (SRA), comprising 27.3 million datasets or 5 × 10 16 basepairs. To realize the potential of the SRA, we constructed Logan, a massive sequence assembly transforming short reads into long contigs and compressing the data over 100-fold, enabling highly efficient petabase-scale analysis. We created Logan-Search, a k -mer index of Logan for free planetary-scale sequence search, returning matches in minutes. We used Logan contigs to identify > 200 million plastic-degrading enzyme homologs, and validate novel enzymes with catalytic activities exceeding current reference standards. Further, we vastly expand the known diversity of proteins (30-fold over UniRef50), plasmids (22-fold over PLSDB), P4 satellites (4.5-fold), and the recently described Obelisk RNA elements (3.7-fold). Logan also enables ecological and biomedical data mining, such as global tracking of antimicrobial resistance genes and the characterization of viral reactivation across millions of human BioSamples. By transforming the SRA, Logan democratizes access to the world’s public genetic data and opens frontiers in biotechnology, molecular ecology, and global health.

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Discussions

• 🌎👩‍🔬 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 [bsky, 218 points, 3 comments]
• Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity doi.org/10.1101/2024... [bsky, 2 points, 0 comments]

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