Assembling the entire SRA into a freely searchable, compressed planetary database, Logan transforms petabyte-scale genomics from intractable to routine—yielding plastic-degrading enzymes that outperform engineered benchmarks and uncovering viral reactivation biology in cell therapies.
The most important insight from Logan is that public sequencing data has become a planetary-scale record of life’s genetic diversity. Until now it has been too large to search and analyze systematically. By assembling nearly the entire public Sequence Read Archive into searchable sequences, Logan turns this archive into a practical discovery engine. In the paper, we show that this enables discoveries ranging from plastic-active enzymes to expanded protein and viral diversity, as well as clinically relevant signals such as viral reactivation in human therapies.
Logan transforms the inaccessible 50-petabase Sequence Read Archive into a searchable 0.9-petabase assembly resource that enables planetary-scale genomic discovery, demonstrating practical utility through identification of superior plastic-degrading enzymes, characterization of viral reactivation in clinical cell therapies, and order-of-magnitude expansions in the known diversity of proteins, plasmids, and viral elements.
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 × 1016 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.