ALEA incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic 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.

ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, ALEA generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.

Current Release

ALEA 1.2.2

Released Apr 21, 2015

Fixed a bug for creating allelic tracks using the separate genome method.

Product Package
For Linux (20MB)

User Guide
For all platforms (1.2 MB)

Test Data
For all platforms (10 GB)

Genome Browser Tracks
For all platforms (500 MB)

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