ArticleNature methods2024
Indexing and searching petabase-scale nucleotide resources.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- An extensive morphological and molecular characterization of the neglected class Odontostomatea (Ciliophora).Marine life science & technology · 2026Article
- Segmented filamentous bacteria are worldwide human gut commensals.Nature communications · 2026Article
- A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.bioRxiv : the preprint server for biology · 2026Article
- Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.Science advances · 2026Article
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
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- LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.Nature communications · 2025Article
- Megaplasmids associate withbioRxiv : the preprint server for biology · 2025Article
- Expanded diversity of pedinophytes provides a window into the evolution of the genetic code in organelles.PLoS genetics · 2025Article
- Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.bioRxiv : the preprint server for biology · 2025Article
- A prevalent huge phage clade in human and animal gut microbiomes.bioRxiv : the preprint server for biology · 2025Article
- Metagenomic analysis uncovers novel hepadnaviruses and nackednaviruses.Scientific reports · 2025Article
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- Novel Adomaviruses Associated with Blotchy Bass Syndrome in Black Basses (bioRxiv : the preprint server for biology · 2025Article
- Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae.The ISME journal · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
Searching vast and rapidly growing nucleotide content in resources, such as runs in the Sequence Read Archive and assemblies for whole-genome shotgun sequencing projects in GenBank, is currently impractical for most researchers. Here we present Pebblescout, a tool that navigates such content by providing indexing and search capabilities. Indexing uses dense sampling of the sequences in the resource. Search finds subjects (runs or assemblies) that have short sequence matches to a user query, with well-defined guarantees and ranks them using informativeness of the matches. We illustrate the functionality of Pebblescout by creating eight databases that index over 3.7 petabases. The web service of Pebblescout can be reached at https://pebblescout.ncbi.nlm.nih.gov . We show that for a wide range of query lengths, Pebblescout provides a data-driven way for finding relevant subsets of large nucleotide resources, reducing the effort for downstream analysis substantially. We also show that Pebblescout results compare favorably to MetaGraph and Sourmash.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.