High Performance Computing for Next Generation Sequencing

Posted on 5 April 2012 by Nicola Losito

Next Generation Sequencing has brought unprecedented volumes of data to the bioinformatics arena. Cost reduction in NGS forecasts massive adoption of these technologies by the genome research community. High Performing Computing might be a necessary choice for an efficient processing and analysis of this daunting amount of data. The HPC4NGS SeqAhead workshop presents recent advances in the application of High Performing Computing solutions for NGS. The workshop covers HPC developments for assembly, mapping, RNA-seq, variant analysis, and more and it is targeted to bioinformaticians and computer scientists with interest in NGS.

Organizes: COST Action SeqAhead
Local organizers: Ana Conesa, Ignacio Medina, Joaquín Dopazo
Venue: Centro de Investigación Príncipe Felipe, Valencia, Spain
Registration fee: 70€ (includes material, lunch and coffee breaks)
Registration: http://bioinfo.cipf.es/courses/registration/hpccourse
Further info: aconesa@cipf.es and http://bioinfo.cipf.es/courses/hpc4ngs

Program
21st May

  • 09:00-09:30 Registration and welcome
  • 09:30-10:00 Introduction to HPC for NGS. Juan Manuel Orduña, UV, Spain
  • 10:00-11:00 HPC pipeline for NGS alignment and data analysis. Ignacio Medina, CIPF, Spain
  • 11:00-11:30 Coffee break
  • 11:30-13:00 HPC technologies applied to the BTW transformed to enhance short read assembly. Ignacio Blanquer, UPV, Spain
  • 13:00-14:00 Lunch
  • 14:00-16:00 GPGPU for NGS data analysis. Brian Lam, University of Cambridge, UK
  • 16:00-16:30 Coffee break
  • 16:30-18:00 HPC for de novo assembly. Martin Simonsen, CLC bio, Denmark.

22nd May

  • 09:30-10:15 Speeding up Smith Waterman by SSE/AVX and Open MP Joaquín Tárraga CIPF
  • 10:15-11:00 HPC solutions for Variant Analysis. Cristina Gonzalez, CIPF, Spain
  • 11:00-11:30 Coffee break
  • 11:30-13:00 Parallel programming with StarSs. Rosa Badia, BSC, Spain.
  • 13:00-14:00 Lunch
  • 14:00-16:00 HPC solutions for RNA-seq. Enrique Salvador Quintana, UJI, Spain
  • 16:00-16:30 Coffee break
  • 16:30-17:15 IT infrastructures for NGS data analysis Pablo Escobar, CIPF, Spain
  • 17:15-18:00 The road to the Exabyte TBA, Oscar de Bustos, BULL Spain
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