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

Background: Depth 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. Results: Building 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. Conclusions: SeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.