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GenomicTools | A computational platform for developing high-throughput analytics in genomics

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. Where directly comparable, we evaluated the time and memory performance of GenomicTools against (i) the IRanges Bioconductor package and (ii) the BEDTools suite. In overlap computations, GenomicTools outperforms IRanges and BEDTools with an average 9.1 and 3.6 speedup, respectively in sorted data with a minimal memory footprint.

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GenomicTools forum

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GenomicTools classification

GenomicTools specifications

Unique identifier:
OMICS_02144
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Version:
2.0
Maintained:
Yes
Software type:
Framework/Library
Restrictions to use:
None
Programming languages:
C, C++
Computer skills:
Advanced
Stability:
Stable

GenomicTools distribution

versioning

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No versioning.

GenomicTools support

Documentation

Maintainer

  • Aristotelis Tsirigos <>

Credits

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Publications

Institution(s)

Computational Biology Center, IBM TJ Watson Research Center, Yorktown Heights, NY, USA

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.