Next generation sequencing in cloud computing era
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Some discussion slides from a recent discussion session in Cambridge
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Next generation sequencing in cloud computing era
- 1. Files, Tools, and Bioinformatics in the Cloud Thomas Keane Vertebrate Resequencing Informatics WTSI thomas.keane@sanger.ac.uk Vertebrate Resequencing Informatics 17th November, 2009
- 2. DATA is the problem! NGS means large volumes of raw data Previously SRF (~8-10bytes per bp), now BAM (~1.6bytes per bp) How much data can a sequencing machine produce? 20Gbp per lane, 16 lanes per run (1 run = 1.5 weeks) => 11Tbp/year Small sequencing center: 4 machines? 44Tbp per year! Raw data in BAM: 70Tbytes SV Calling: SVMerge Processed calls much smaller 1000G pilot VCF < 1Gbyte Alignment + BAM improvement Vertebrate Resequencing Informatics 17th November, 2009
- 3. Simplistic Model: Cloud as compute resource Processes 1. Align SRF/Fastq/BAM (2Mbps/sec) Variant calling (n x SNP callers, n indel callers, SV callers) Sequencing Center/Institute BAM + VCF (2Mbps/sec) BAM 3,240 days VCF to upload! Vertebrate Resequencing Informatics 17th November, 2009
- 4. Move the raw data generation to the compute Variant calling (n x SNP callers, n indel callers, SV callers) Sequencing Center/Institute VCF BAM VCF Vertebrate Resequencing Informatics 17th November, 2009
- 5. Large Collaborative Projects: Cloud centric model VCF Analysis groups Vertebrate Resequencing Informatics 17th November, 2009