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

Saket Choudhary
2019 F1000Research  
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,
more » ... tilizing 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.
doi:10.12688/f1000research.18676.1 pmid:31114675 pmcid:PMC6505635 fatcat:c3xt7xuqurabdmha3yyaracff4