Chapter 1: Raw read Archives and Cloud Services

Raw read Archives and Cloud services – SRA (Sequence Read Archive) and Illumina Basespace

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Introduction to SRA- https://www.ncbi.nlm.nih.gov/sra

Sequence Read Archive (SRA) makes biological sequence data available to the research community

• Enhance reproducibility

• Allow for new discoveries by comparing data sets

• The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms, including

  • Roche 454 GS System
  • Illumina Genome Analyzer
  • Applied Biosystems SOLiD System
  • Helicos Heliscope
  • Complete Genomics
  • Pacific Biosciences SMRT
  • Oxford Nanopore Minion sequencer???

• Submitting data to SRA

• SRA Toolkit

  • fastq-dump Converts SRA data into fastq format
  • prefetch Allows command-line downloading of SRA

• Data growth

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Introduction to Illumina Basespace

Basespace is a cloud-based genomic analysis and storage platform

• Set up runs for Illumina sequencer
• Remote monitoring for a sequence run
• Stream data to cloud-storage directly from the sequencer
• Analyze data with pre-configured Bioinformatics pipeline
• Make data sharing and downloading easy