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: SeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.
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:SeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.
Authors: Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo Journal: Genome Res Date: 2010-07-19 Impact factor: 9.043
Authors: Tomasz Gambin; Zeynep C Akdemir; Bo Yuan; Shen Gu; Theodore Chiang; Claudia M B Carvalho; Chad Shaw; Shalini Jhangiani; Philip M Boone; Mohammad K Eldomery; Ender Karaca; Yavuz Bayram; Asbjørg Stray-Pedersen; Donna Muzny; Wu-Lin Charng; Vahid Bahrambeigi; John W Belmont; Eric Boerwinkle; Arthur L Beaudet; Richard A Gibbs; James R Lupski Journal: Nucleic Acids Res Date: 2017-02-28 Impact factor: 16.971
Authors: Abhinav Nellore; Leonardo Collado-Torres; Andrew E Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T Leek; Ben Langmead Journal: Bioinformatics Date: 2017-12-15 Impact factor: 6.937