Pebblescout is an easy-to-use tool for fast sequence search in petabase-scale nucleotide resources
Author:
Funder
This work was carried out by staff of the National Library of Medicine (NLM), National Institutes of Health, with support from NLM.
Publisher
Springer Science and Business Media LLC
Link
https://www.nature.com/articles/s41592-024-02281-y.pdf
Reference5 articles.
1. Zheludev, I. N. et. al. Viroid-like colonists of human microbiomes. Preprint at bioRxiv https://doi.org/10.1101/2024.01.20.576352 (2024). A preprint that presents a previously unrecognized class of viroid-like elements.
2. Mario-Vasquez, J. E. et al. Finding Candida auris in public metagenomic repositories. PLoS One https://doi.org/10.1371/journal.pone.0291406 (2024). This paper reports on monitoring systems for Candida auris using publicly available metagenomic data in the SRA.
3. Joakim Larsson, D. G. & Flach, C.-F. Antibiotic resistance in the environment. Nat. Rev. Microbiol. 20, 257–269 (2022). A review article that presents the global health challenge of antibiotic resistance; it includes a discussion on methods for surveillance and an assessment of potential drivers.
4. Karasikov, M. et al. Lossless indexing with counting de Bruijn graphs. Genome Res. 32, 1754–1764 (2022). An article that presents counting de Bruijn graphs with positional annotations and the Virus PacBio HiFi dataset.
5. Pierce, N. T. et al. Large-scale sequence comparisons with Sourmash. F1000Research 8, 1006 (2019). An article that presents the k-mer analysis tool Sourmash.
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