绿洲：跨越表达水平动态范围的稳健从头 RNA-seq 组装。

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

机构信息

Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

出版信息

Bioinformatics. 2012 Apr 15;28(8):1086-92. doi: 10.1093/bioinformatics/bts094. Epub 2012 Feb 24.

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/.

动机

高通量测序使得新模型生物的分析变得更加经济实惠。虽然组装新的基因组仍然可能很昂贵和困难，但使用 RNA-seq 对 mRNA 进行测序是可行的。在没有已知基因组的情况下，有必要从头开始组装这些序列，同时考虑可能的替代异构体和表达值的动态范围。

结果

我们提出了一个名为 Oases 的软件包，旨在在没有参考基因组的情况下，针对广泛的表达值和存在替代异构体的情况，通过使用一系列哈希长度、噪声的动态过滤、对替代剪接事件的稳健解析以及多个组装的高效合并，对 RNA-seq reads 进行启发式组装。它在人类和小鼠的 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有显著的改进。