Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

Matthew N. Bernstein; Ariella L. Gladstein; Khun Zaw Latt; Emily Clough; Ben Busby; Allissa Dillman

doi:https://doi.org/10.12688/f1000research.23180.2

doi.org/10.12688/f1000research.23180.2

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

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..., Allissa Dillman

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F1000Research

Volume: 9, Pages: 376 - 376

Published: Aug 4, 2020

Abstract

The Sequence Read Archive (SRA) is a large public repository that stores raw next-generation sequencing data from thousands of diverse scientific investigations. Despite its promise, reuse and re-analysis of SRA data has been challenged by the heterogeneity and poor quality of the metadata that describe its biological samples. Recently, the MetaSRA project standardized these metadata by annotating each sample with terms from biomedical...

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Paper Details

Title

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

DOI

doi.org/10.12688/f1000research.23180.2

Published Date

Aug 4, 2020

Journal

F1000Research

Volume

9

Pages

376 - 376

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