We have just released elPrep, a high-performance tool for preparing SAM/BAM/CRAM files in sequencing pipelines. It can be used as a replacement for standard tools, such as SAMtools and Picard, for preparation steps such as sorting, marking duplicates, reordering contigs, and so on, while producing identical results. elPrep is designed as a multi-threaded applications that runs entirely in memory, avoids repeated file I/O, and merges the computations of several preparation steps, to speed up the execution time by an order of magnitude: benchmarks show elPrep is 10-25x faster than SAMtools and Picard, depending on the number of cores used. elPrep is also a modular, extensible framework, where users can easily add more preparation steps that automatically take advantage of elPrep’s inherent parallelism and performance.
Check out all the software released by the lab on our Software page.
- Invited talk on elPrep at the (IB)² Seminar on March 20, 2015
- New results and software on HPC sparse computation published
- Videos from the “High Performance Computing (HPC) for Life Sciences” event now available
- Jörg Kurt Wegner (Johnson & Johnson) giving closing keynote at EuroQSAR 2014
- Tutorial on GASPI, the PGAS API