STAR: ultrafast universal RNA-seq aligner STAR：超快的通用RNA-seq比对器

STAR：超快的通用RNA-seq比对器

动机：因为不连续的转录本结构，相对短的片段长度，和测序技术持续增加的通量，高通量RNA-seq数据的准确比对是一个有挑战性且仍未解决的问题。当前可用的RNA-seq比对器遭受高比对错误率，低比对速度，片段长度限制和比对偏差。结果：为了比对我们的大量（> 800亿片段）ENCODE转录组RNA-seq数据集，我们基于一种以前未描述的RNA-seq比对算法开发了STAR（Spliced Transcripts Alignments to a Reference，STAR）软件，该算法使用了未压缩后缀阵列中的连续最大可比对种子搜索，接着种子聚类和缝合过程。STAR在比对速度上胜过其他比对器50多倍，在一个普通的12核服务器上，每小时比对5.5亿2 x 76 bp双端片段到人类基因组上，同时改进了比对敏感性和准确性。除了典型剪接的非偏从头检测外，STAR能够发现非典型拼接和嵌合（融合）转录本，并能够比对全长RNA序列。使用逆转录聚合酶链式反应扩增子的罗氏454测序，我们实验上验证了1960个新的基因间剪接点，具有80-90%的准确率，证实了STAR比对策略的高准确性。可用性和实现：STAR被实现为一个单机C++代码。STAR是在GPLv3许可证下发布的免费开源软件，能够从https://github.com/alexdobin/STAR/下载。

STAR: ultrafast universal RNA-seq aligner

Dobin Alexander   Davis Carrie A   Schlesinger Felix   Drenkow Jorg   Zaleski Chris  

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/.