Michael Gerth
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How to efficiently bulk download NGS data from sequence read databases

25/2/2018

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This blog post deals with the various ways of downloading large amounts of sequencing data (e.g., from NCBI’s SRA database). When I needed to bulk download short read for a recent project, it took me some time to figure out how to achieve this efficiently, and I am sharing my experience here in the hope it might be useful. 

The problem: you want to download lots of sequencing data (typically in form of Illumina generated reads), e.g., to reproduce a published experiment. The amount of data makes it impossible to click+download through a browser interface. There are two potential solutions: 1) download via NCBI’s SRA toolkit, and 2) access ftp servers directly.  

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    This is the website of Michael Gerth. I am a biologist with an interest in insects and the microbes within them. Click here to learn more.

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  • News & Blog
  • About
  • Research
    • Experimental evolution of Spiroplasma after host shifts
    • Wolbachia phylogenomics
    • Rickettsial symbionts in green lacewings
    • The role of Wolbachia in quill mites
    • Methods in molecular phylogenetics
  • Publications
  • Resources