STAR: ultrafast universal RNA-seq aligner

A Dobin, CA Davis, F Schlesinger, J Drenkow… - …, 2013 - academic.oup.com
A Dobin, CA Davis, F Schlesinger, J Drenkow, C Zaleski, S Jha, P Batut, M Chaisson
Bioinformatics, 2013academic.oup.com
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet
unsolved problem because of the non-contiguous transcript structure, relatively short read
lengths and constantly increasing throughput of the sequencing technologies. Currently
available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read
length limitation and mapping biases. Results: To align our large (> 80 billon reads)
ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment …
Abstract
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
Results: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80–90% success rate, corroborating the high precision of the STAR mapping strategy.
Availability and implementation: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
Contact:  dobin@cshl.edu.
Oxford University Press