Psst! I've posted some details about my notebook setup here.

Streaming data from the SRA with fastq-dump

NCBI's Sequence Read Archive is the go-to repository for published genome-scale sequence data sets. Although there are a variety of ways to download sequence data from SRA, the fastq-dump command from the SRA Toolkit is the most convenient in my opinion. In fact, with a few settings tweaks fastq-dump can stream data directly from the SRA into an analysis ...

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That darn cache! Configuring the SRA Toolkit

Permalink: 2016-05-18 by Daniel S. Standage in blog tags: sra ngs

Last night I started a batch job on our group's cluster to download and process 9 Illumina libraries from the NCBI SRA. In the past, I have almost always downloaded such data via direct links to .sra files on the SRA FTP site, and then converted these files to Fastq format using the fastq-dump command from the SRA Toolkit ...

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