TY - JOUR T1 - SeQuiLa-cov: A fast and scalable library for depth of coverage calculations JF - bioRxiv DO - 10.1101/494468 SP - 494468 AU - Marek Wiewiórka AU - Agnieszka Szmurło AU - Wiktor Kuśmirek AU - Tomasz Gambin Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/12/13/494468.abstract N2 - 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.List of AbbreviationsAPI –Application Programming InterfaceBAM –Binary Alignment MapGKL –Genomics Kernel LibraryNGS –Next Generation SequencingSQL –Structured Query LanguageYARN –Yet Another Resource NegotiatorWES –Whole Exome SequencingWGS –Whole Genome Sequencing ER -