This is an old revision of the document!


ASEQ - fast allele-specific studies from next-generation sequencing data


DESCRIPTION

Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. Such studies often present with computationally challenging burdens that hinder genome-wide investigations across large datasets that are now becoming available through the 1,000 Genomes Project and The Cancer Genome Atlas (TCGA) initiatives. ASEQ is a tool to perform gene-level allele-specific expression (ASE) analysis from paired genomic and transcriptomic NGS data without requiring paternal and maternal genome data. It offers an easy-to-use set of modes that transparently to the user takes full advantage of a built-in fast computational engine. ASEQ can be used to rapidly and reliably screen large NGS datasets for the identification of allele specific features and can be integrated in any NGS pipeline and runs on computer systems with multiple CPUs, CPUs with multiple cores or across clusters of machines.

REFERENCES


INSTALL

BASIC USAGE

REQUIREMENTS

CLONET requires Linux kernel >= 2.6.15. CLONET requires R >= 2.7 and the following packages, parallel, dgof, sets, and pso, igraph, reshape2. CLONET requires global folder names. CLONET recommends ASEQ tool to generate initial pileup analysis (binaries provided).


Code by Alessandro Romanel
Laboratory of Computational Oncology (F. Demichelis)
Centre for Integrative Biology, University of Trento, Italy
email contacts: romanel@science.unitn.it; demichelis@science.unitn.it

ASEQ is distributed under the MIT Licence.

DOWNLOADS

Current version 1.1.8