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bioRxiv · 10.1101/494468

SeQuiLa-cov: A fast and scalable library for depth of coverage calculations

Wiewiorka, M.·Szmurlo, A.·Kusmirek, W.·Gambin, T.
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Abstract

BackgroundDepth of coverage calculation is an important and computationally intensive preprocessing step in a variety of next generation sequencing pipelines, including the analyses of RNA-seq data, detection of copy number variants, or quality control procedures.\n\nResultsBuilding upon big data technologies, we have developed SeQuiLa-cov, an extension to the recently released SeQuiLa platform, which provides efficient depth of coverage calculations, reaching more than 100x speedup over the state-of-the-art tools. Performance and scalability of our solution allows for exome and genome-wide calculations running locally or on a cluster while hiding the complexity of the distributed computing with Structured Query Language Application Programming Interface.\n\nConclusionsSeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.

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Wiewiorka, M., Szmurlo, A., Kusmirek, W., Gambin, T.. 2018-12-13. SeQuiLa-cov: A fast and scalable library for depth of coverage calculations. https://doi.org/10.1101/494468

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