GROK (Genomic Region Operation Toolkit) is "Swiss Army knife" library for processing genomic interval data. GROK operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.
Download
- User Guide (PDF)
- Python, Lua, command line and C++ API: source package (GROK 1.1.1)
- R: Linux/Mac package (GROK 1.1.1)
- Changelog
Installation instructions are in User Guide. Currently, GROK supports Unix-like systems and has been tested in Linux.
Old versions
The following downloads are archives of old GROK versions.
Citation
If you use GROK, please cite the following article:Ovaska K, Lyly L, Sahu B, Janne OA, Hautaniemi S. Genomic region operation kit for flexible processing of deep sequencing data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013 Jan 9
Credits
- Kristian Ovaska, kristian.ovaska (at) helsinki.fi, developer, technical contact
- Lauri Lyly, lauri.lyly (at) helsinki.fi, developer
- Sampsa Hautaniemi, sampsa.hautaniemi (at) helsinki.fi, coordinator
Copyright (c) 2011-2013, Systems Biology Laboratory. All rights reserved. GROK is licensed under the BSD license.
See README file in the source distribution for credits and copyright notices of bundled software.
Updated 2013-07-03