Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
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DOI：
10.1093/bioinformatics/bts094
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发表时间：
2012-04-15
期刊：
影响因子：
--
通讯作者：
Birney E
中科院分区：
文献类型：
--
作者：
Schulz MH;Zerbino DR;Vingron M;Birney E
动机：高通量测序使新模式生物的分析更加经济实惠。尽管组装新的基因组仍然昂贵且困难，但使用RNA-seq对mRNA进行测序是可能的。在缺乏已知基因组的情况下，有必要重新组装这些序列，同时考虑可能的替代同种型和表达值的动态范围。结果如下：我们提出了一个名为Oases的软件包，该软件包旨在在没有参考基因组的情况下，在广泛的表达值范围内以及在存在替代亚型的情况下，精确地组装RNA-seq读数。它通过使用哈希长度阵列、噪声的动态过滤、选择性剪接事件的鲁棒分辨率和多个组件的有效合并来实现这一点。它在人和小鼠RNA-seq数据上进行了测试，并显示在transABySS和Trinity从头转录组组装器上显著改善。可用性和实施：Oases在GPL许可下可在www.example.com上免费获得dzerbino@ucsc.edu方式：www.ebi.ac.uk/~zerbino/oases/补充信息：补充数据可在生物信息学在线上获得。
Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values. Results: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers. Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/ Contact: dzerbino@ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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