ALEA: a toolbox for allele-specific epigenomics analysis

The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. A team led by researchers at the BC Cancer Agency, Canada have deic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data.


AVAILABILITY: package, test data, and usage instructions are available at


Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ. (2013) ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics [Epub ahead of print]. [abstract]