Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes
- 1The Pennsylvania State University
Abstract
Recent efforts have demonstrated that systematic analysis of the millions of metagenomes in the Sequence Read Archive (SRA) enables groundbreaking biological discoveries. However, SRA-scale comparison of whole metagenomes has remained elusive. Here, we introduce the most comprehensive resource to date for experiment-to-experiment analysis of all SRA metagenomes, comprising FracMinHash sketches (470GB), hypergen sketches (19GB), and an all-pairs Jaccard similarity matrix (90GB), which we release online at https://github.com/RolandFaure/SRA-metagenome-sketches-databases. These resources enable a wide range of analyses, which we demonstrate with several applications. First, we use the FracMinHash sketches to uncover temporal trends, finding that the amount of newly discovered microbial sequence continues to grow, rather than saturate or shrink. Second, we use the hypergen sketches, which enable nearest-neighbor search, to identify co-assembly candidates and thereby improve assembly quality. Third, we use the similarity matrix to analyze all SRA metagenomes, identifying duplicated submissions and over 50K candidates for metadata correction. Together, our resources unlock systematic analysis of metagenomic data at unprecedented scale.
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BibTeX
@misc{faure2026sketching,
title = {{Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes}},
author = {R. Faure and A. H. Nakshi and M. H. Abrar and R. Chikhi and T. Lemane and M. Taheri and S. Won and H. Wu and D. Koslicki and P. Medvedev},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.07.757297},
url = {https://www.biorxiv.org/content/10.64898/2026.10.07.757297v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes
AU - R. Faure
AU - A. H. Nakshi
AU - M. H. Abrar
AU - R. Chikhi
AU - T. Lemane
AU - M. Taheri
AU - S. Won
AU - H. Wu
AU - D. Koslicki
AU - P. Medvedev
PY - 2026
DA - 2026/10/07
PB - bioRxiv
DO - 10.64898/2026.10.07.757297
UR - https://www.biorxiv.org/content/10.64898/2026.10.07.757297v1
AB - Recent efforts have demonstrated that systematic analysis of the millions of metagenomes in the Sequence Read Archive (SRA) enables groundbreaking biological discoveries. However, SRA-scale comparison of whole metagenomes has remained elusive. Here, we introduce the most comprehensive resource to date for experiment-to-experiment analysis of all SRA metagenomes, comprising FracMinHash sketches (470GB), hypergen sketches (19GB), and an all-pairs Jaccard similarity matrix (90GB), which we release online at https://github.com/RolandFaure/SRA-metagenome-sketches-databases. These resources enable a wide range of analyses, which we demonstrate with several applications. First, we use the FracMinHash sketches to uncover temporal trends, finding that the amount of newly discovered microbial sequence continues to grow, rather than saturate or shrink. Second, we use the hypergen sketches, which enable nearest-neighbor search, to identify co-assembly candidates and thereby improve assembly quality. Third, we use the similarity matrix to analyze all SRA metagenomes, identifying duplicated submissions and over 50K candidates for metadata correction. Together, our resources unlock systematic analysis of metagenomic data at unprecedented scale.
ER -