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

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

SUBMITTER: Taylor LJ 

PROVIDER: S-EPMC7267817 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature