Display options
Cite
Taylor LJ, Abbas A, Bushman FD. grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories. Bioinformatics. 2020;36(11):3607-3609doi: 10.1093/bioinformatics/btaa167.
Taylor, L. J., Abbas, A., & Bushman, F. D. (2020). grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories. Bioinformatics (Oxford, England), 36(11), 3607-3609. https://doi.org/10.1093/bioinformatics/btaa167
Taylor, Louis J, et al. "grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories." Bioinformatics (Oxford, England) vol. 36,11 (2020): 3607-3609. doi: https://doi.org/10.1093/bioinformatics/btaa167
Taylor LJ, Abbas A, Bushman FD. grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories. Bioinformatics. 2020 Jun 01;36(11):3607-3609. doi: 10.1093/bioinformatics/btaa167. PMID: 32154830; PMCID: PMC7267817.
Copy Download .nbib Format: NLM
Share it on

Bioinformatics. 2020 Jun 01;36(11):3607-3609. doi: 10.1093/bioinformatics/btaa167.

grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories.

Bioinformatics (Oxford, England)

Louis J Taylor, Arwa Abbas, Frederic D Bushman

Affiliations

  1. Department of Microbiology, Perelman School of Medicine, University of Pennsylvania.
  2. Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

PMID: 32154830 PMCID: PMC7267817 DOI: 10.1093/bioinformatics/btaa167

Abstract

SUMMARY: High-throughput sequencing is a powerful technique for addressing biological questions. Grabseqs streamlines access to publicly available metagenomic data by providing a single, easy-to-use interface to download data and metadata from multiple repositories, including the Sequence Read Archive, the Metagenomics Rapid Annotation through Subsystems Technology server and iMicrobe. Users can download data and metadata in a standardized format from any number of samples or projects from a given repository with a single grabseqs command.

AVAILABILITY AND IMPLEMENTATION: Grabseqs is an open-source tool implemented in Python and licensed under the MIT license. The source code is freely available at https://github.com/louiejtaylor/grabseqs, the Python Package Index and Anaconda Cloud repository.

CONTACT: [email protected].

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: [email protected].

References

  1. Nat Biotechnol. 2019 Dec;37(12):1408-1412 - PubMed
  2. Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544 - PubMed
  3. Ecohealth. 2015 Dec;12(4):726-35 - PubMed
  4. Nat Methods. 2018 May;15(5):359-362 - PubMed
  5. Nat Methods. 2012 Mar 04;9(4):357-9 - PubMed
  6. Cell. 2019 Jan 24;176(3):649-662.e20 - PubMed
  7. F1000Res. 2019 Apr 23;8:532 - PubMed
  8. Nat Methods. 2017 Oct;14(10):959-962 - PubMed
  9. Cell Host Microbe. 2019 May 8;25(5):719-729.e4 - PubMed
  10. Genome Res. 2014 Jul;24(7):1180-92 - PubMed
  11. Nucleic Acids Res. 2016 Jan 4;44(D1):D48-50 - PubMed
  12. Microbiome. 2019 Mar 22;7(1):46 - PubMed
  13. Nature. 2018 Jun;558(7709):307-312 - PubMed
  14. Nat Commun. 2014 Jul 24;5:4498 - PubMed

MeSH terms

Publication Types

Grant support