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ASEQ - fast allele-specific studies from next-generation sequencing data
DESCRIPTION
Single base level information from next-generation sequencing (NGS) potentially allow for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells that have remained unexplored. Such studies often present with computationally challenging burdens that might hinder genome-wide investigations across large datasets that are now publicly available such as the 1,000 Genomes Project data and The Cancer Genome Atlas (TCGA). We present ASEQ, a tool to perform gene-level allele-specific expression (ASE) analysis from paired genomic and transcriptomic NGS data without requiring information from the paternal or maternal genome. ASEQ offers an easy-to-use set of functionalities that take full advantage of a fast computational engine by combining multi-threaded computation and high performing samtools APIs. ASEQ can be used to rapidly and reliably screen large NGS datasets for the identification of allele specific features. It can be integrated in any NGS pipeline and runs on computer systems with multiple CPUs, CPUs with multiple cores, or across clusters of machines and cloud computing platforms.