From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

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Abstract

The aim of this tutorial is twofold:

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?
How can you process a batch of sequencing data from several samples efficiently/in parallel with Galaxy?
Starting from raw sequenced reads of whole-genome sequenced samples of SARS-CoV-2, how can you identify mutations in the genomes of these samples?

Understand how Galaxy and the Sequence Read Archive interact
Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send selected metadata to Galaxy, and then import sequence data from SRA into Galaxy
Understand how collections enable processing of sequencing data in batches
Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples

Licence: Creative Commons Attribution 4.0 International

Keywords: Variant Analysis, covid19, one-health, virology

Target audience: Students

Resource type: e-learning

Version: 16

Status: Active

Prerequisites:

Learning objectives:

Understand how Galaxy and the Sequence Read Archive interact
Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send selected metadata to Galaxy, and then import sequence data from SRA into Galaxy
Understand how collections enable processing of sequencing data in batches
Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples

Date modified: 2024-06-14

Date published: 2020-06-24

Authors: Anton Nekrutenko, Daniel Blankenberg, Dave Clements, Marius van den Beek

Contributors: Wolfgang Maier

Scientific topics: Genetic variation

External resources: