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.

elPrep is now available as an open source project on GitHub.  We also provide a demo, including test data. The API documentation provides details about the elPrep framework.

Check out all the software released by the lab on our Software page.


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