STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras

This paper introduces STAR (Spliced Transcripts Alignment to a Reference), an ultrafast RNA-seq aligner that achieves high alignment accuracy by using uncompressed suffix arrays together with a novel sequential maximum mappable seed search strategy. STAR can align both short and long reads at speeds an order of magnitude faster than contemporary tools while maintaining splice junction discovery capabilities.