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

ABSTRACT:

Background

Depth of coverage calculation is an important and computationally intensive preprocessing step in a variety of next-generation sequencing pipelines, including the analysis of RNA-sequencing 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 >100× speedup over the state-of-the-art tools. The performance and scalability of our solution allow 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

SUBMITTER: Wiewiorka M 

PROVIDER: S-EPMC6680061 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature