GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-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 from preprocessing and quality control to meta-analyses. More specifically, the user can easily create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications.
In addition to enabling rapid prototyping, the GenomicTools platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. Finally, the GenomicTools platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.
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
- Tsirigos A, Haiminen N, Bilal E, Utro F. (2011) GenomicTools: a computational platform for developing high-throughput analytics in genomics. Bioinformatics [Epub ahead of print]. [abstract]