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Pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

ABSTRACT: The NCBI Sequence Read Archive (SRA) is the primary archive of next-generation sequencing datasets. SRA makes metadata and raw sequencing data available to the research community to encourage reproducibility and to provide avenues for testing novel hypotheses on publicly available data. However, methods to programmatically access this data are limited. We introduce the Python package, pysradb, which provides a collection of command line methods to query and download metadata and data from SRA, utilizing the curated metadata database available through the SRAdb project. We demonstrate the utility of pysradb on multiple use cases for searching and downloading SRA datasets. It is available freely at https://github.com/saketkc/pysradb.

SUBMITTER: Choudhary S

PROVIDER: S-EPMC6505635 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

Choudhary Saket S

F1000Research 20190423

The NCBI Sequence Read Archive (SRA) is the primary archive of next-generation sequencing datasets. SRA makes metadata and raw sequencing data available to the research community to encourage reproducibility and to provide avenues for testing novel hypotheses on publicly available data. However, methods to programmatically access this data are limited. We introduce the Python package, pysradb, which provides a collection of command line methods to query and download metadata and data from SRA, u ...[more]

PMID: 31114675

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