The title of the talk is elPrep: high-performance preparation of sequence alignment/map files for variant calling:
elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline. elPrep is designed as a multi-threaded application that runs entirely in memory, avoids repeated file I/O, and merges the computation of several preparation steps to speed up the execution time by an order of magnitude. For example, for a preparation pipeline of 5 steps on an 8GB exome BAM file, we reduce the execution time from 2.5 hours, when using a combination of SAMtools and Picard, to less than 25 minutes when using elPrep, while utilising the same server resources. For a standard pharmaceutical experiment consisting of 150+ of such BAM files, elPrep thus removes several hundreds of hours of computing time.
The location of the event is:
Feel free to drop in !
- 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