NGS goes HPC - Next Generation Sequencing-Datenanalyse auf HPC-Infrastrukturen

Next generation sequencing(NGS) technologies decode genome sequences in ever shorter time. Current software for de novo assembly of short reads does not meet the requirements of the increasing data volume. Goals of the project are therefore to accelerate de novo assembly algorithms by utilizing different levels of parallelism (shared memory, distributed memory, hardware accelerators) and the development of efficient visualization methods. The publication of the algorithms is planed as open source library.

Partners

Bull GmbH, Köln
Forschungszentrum Jülich GmbH
Max-Planck-Institut für Biologie des Alterns, Köln
Biotechnologischen Zentrum (BIOTEC), TU-Dresden
Zentrum für Informationsdienste und Hochleistungsrechnen, TU-Dresden
Regional Computing Center (RRZK), Universität zu Köln
Cologne Center for Genomics (CCG), Universität zu Köln
DataDirect Networks GmbH, Freiburg
Intel’s ExaCluster Laboratory, Jülich

Project Website

http://ngsgoeshpc.uni-koeln.de/

Project Term

06/2011 - 05/2014

Funding

BMBF

Publications

Robert Henschel, Matthias Lieber, Le-Shin Wu, Phillip M. Nista, Brian J. Haas, Richard D. LeDuc. Trinity RNA-Seq Assembler Performance Optimization. Published in XSEDE'12 proceedings, 2012.