MOTIVATION: Recent advances in sequencing technology have resulted in the dramatic increase of sequencing data, which, in turn, requires efficient management of computational resources, such as computing time, memory requirements as well as prototyping of computational pipelines. RESULTS: We present GenomicTools, a flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. GenomicTools implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks ranging from pre-processing and quality control to meta-analyses. Additionally, the GenomicTools platform is designed to analyze large datasets of any size by minimizing memory requirements. In practical applications, where comparable, GenomicTools outperforms existing tools in terms of both time and memory usage. AVAILABILITY: The GenomicTools platform (version 2.0.0) was implemented in C++. The source code, documentation, user manual, example datasets and scripts are available online at http://code.google.com/p/ibm-cbc-genomic-tools.
MOTIVATION: Recent advances in sequencing technology have resulted in the dramatic increase of sequencing data, which, in turn, requires efficient management of computational resources, such as computing time, memory requirements as well as prototyping of computational pipelines. RESULTS: We present GenomicTools, a flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. GenomicTools implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks ranging from pre-processing and quality control to meta-analyses. Additionally, the GenomicTools platform is designed to analyze large datasets of any size by minimizing memory requirements. In practical applications, where comparable, GenomicTools outperforms existing tools in terms of both time and memory usage. AVAILABILITY: The GenomicTools platform (version 2.0.0) was implemented in C++. The source code, documentation, user manual, example datasets and scripts are available online at http://code.google.com/p/ibm-cbc-genomic-tools.
Authors: Michael P Lisanti; Aristotelis Tsirigos; Stephanos Pavlides; Kimberley Jayne Reeves; Maria Peiris-Pagès; Amy L Chadwick; Rosa Sanchez-Alvarez; Rebecca Lamb; Anthony Howell; Ubaldo E Martinez-Outschoorn; Federica Sotgia Journal: Cell Cycle Date: 2013-12-05 Impact factor: 4.534
Authors: Chun Yew Fong; Omer Gilan; Enid Y N Lam; Alan F Rubin; Sarah Ftouni; Dean Tyler; Kym Stanley; Devbarna Sinha; Paul Yeh; Jessica Morison; George Giotopoulos; Dave Lugo; Philip Jeffrey; Stanley Chun-Wei Lee; Christopher Carpenter; Richard Gregory; Robert G Ramsay; Steven W Lane; Omar Abdel-Wahab; Tony Kouzarides; Ricky W Johnstone; Sarah-Jane Dawson; Brian J P Huntly; Rab K Prinjha; Anthony T Papenfuss; Mark A Dawson Journal: Nature Date: 2015-09-14 Impact factor: 49.962
Authors: Omer Gilan; Enid Y N Lam; Isabelle Becher; Dave Lugo; Ester Cannizzaro; Gerard Joberty; Aoife Ward; Meike Wiese; Chun Yew Fong; Sarah Ftouni; Dean Tyler; Kym Stanley; Laura MacPherson; Chen-Fang Weng; Yih-Chih Chan; Margherita Ghisi; David Smil; Christopher Carpenter; Peter Brown; Neil Garton; Marnie E Blewitt; Andrew J Bannister; Tony Kouzarides; Brian J P Huntly; Ricky W Johnstone; Gerard Drewes; Sarah-Jane Dawson; Cheryl H Arrowsmith; Paola Grandi; Rab K Prinjha; Mark A Dawson Journal: Nat Struct Mol Biol Date: 2016-06-13 Impact factor: 15.369
Authors: Panagiotis Ntziachristos; Aristotelis Tsirigos; Pieter Van Vlierberghe; Jelena Nedjic; Thomas Trimarchi; Maria Sol Flaherty; Dolors Ferres-Marco; Vanina da Ros; Zuojian Tang; Jasmin Siegle; Patrik Asp; Michael Hadler; Isaura Rigo; Kim De Keersmaecker; Jay Patel; Tien Huynh; Filippo Utro; Sandrine Poglio; Jeremy B Samon; Elisabeth Paietta; Janis Racevskis; Jacob M Rowe; Raul Rabadan; Ross L Levine; Stuart Brown; Francoise Pflumio; Maria Dominguez; Adolfo Ferrando; Iannis Aifantis Journal: Nat Med Date: 2012-02-06 Impact factor: 53.440