SeqAhead Workshop on High Performance Computing for Next Generation Sequencing Analysis (HPC4NGS)

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

Registration fee: 70€  (includes material, lunch and coffee breaks)

Registration:  http://bioinfo.cipf.es/courses/registration/hpccourse

Further info: aconesacipf [dot] es and http://bioinfo.cipf.es/courses/hgc4ngs

Venue: Centro de Investigación Príncipe Felipe, Valencia, Spain (click here for accomodation options)

Dinner doodle: http://www.doodle.com/hga3s9233p6ht5qn

Program

21st May

09:00-09:30 Registration and welcome

09:30-10:00 Introduction to HPC technologies. Juan Manuel Orduña, UV, Spain

10:00-11:00 HPC pipeline and cloud-based solutions for NGS data analysis. Ignacio Medina, CIPF, Spain

11:00-11:30 Coffee break

11:30-12:15 HPC solutions for Genomics Variant Analysis. Cristina Gonzalez, CIPF, Spain

12:15-13:00 Speeding up Smith Waterman algorithm using SSE/AVX and OpenMP Joaquín Tárraga CIPF

13:00-14:00 Lunch

14:00-16:00 GPGPU for NGS data analysis. Brain 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

09:30-11:00 Parallel programming with StarSs. Rosa Badia, BSC, Spain.

11:00-11:30 Coffee break

11:30-13:00 HPC technologies applied to the Burrows-Wheeler Transform (BWT) to enhance short read assembly. Ignacio Blanquer, UPV, Spain

13:00-14:00 Lunch

14:00-15:00 HPC solutions for RNA-seq. Enrique Salvador Quintana, UJI, Spain

15:00-16:00 Genome-wide nucleosome positioning using Next Generation Sequencing and High Peformance Computing: from peaks to reads. Oscar Flores, BSC, 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. Oscar de Bustos, BULL, Spain