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HSA: A Heuristic Splice Alignment Tool

机译：HSA：启发式拼接对齐工具

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BackgroundRNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons.MethodsA two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner - BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match.ResultsCompare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent.ConclusionsHSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.
机译：BackgroundRNA-Seq方法是一种革命性的转录组学测序技术，是下一代测序（NGS）的代表。借助RNA-Seq的高通量测序，我们可以从深度序列分析和数据挖掘中获取更多信息，例如差异表达和新型剪接变体。但是短的读取长度给比对带来了很大的挑战，尤其是当读取跨越两个或多个外显子时。方法在本研究中生成了两步启发式剪接比对工具。首先，将原始读取映射到使用未拼接的对齐器-BWA的引用;其次，将初始未映射的读段拆分为三个相等的短读段（种子），将每个种子与参考对齐，过滤命中，搜索可能的拆分读段位置并将扩展命中扩展为完全匹配。结果与其他拼接对齐工具（例如SOAPsplice和Tophat2）进行比较HSA在呼叫速率和效率方面具有更好的性能，但其结果在某种程度上不如其他软件准确。结论HSA是RNA-Seq读取映射的有效剪接比对仪，可从https://github.com获得。 / vlcc / HSA。

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