基于压缩感知的合并序列数据精确解码
Accurate Decoding of Pooled Sequenced Data Using Compressed Sensing
摘要：
为了克服DNA条形码在当前一代高通量测序仪器中多路复用大量样品时所施加的限制，我们最近提出了一种新的方案，该方案利用了组合池设计（组测试）doi：10.1371/journal. pcbi. 1003010的进步。我们还展示了这种新方案如何使从头选择性测序和组装大型，高度重复的基因组成为可能。在这里，我们解决的问题，从这样的协议获得的解码池测序数据。我们的算法采用了压缩感知和纠错码解码的思想的协同组合。水稻基因组的合成数据和大麦基因组的真实数据的实验结果表明，我们的新的解码算法，使显着更高的质量组装比以前的方法。
英文摘要：
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances in combinatorial pooling design (group testing) doi:10.1371/journal.pcbi.1003010. We have also demonstrated how this new protocol would enable de novo selective sequencing and assembly of large, highly-repetitive genomes. Here we address the problem of decoding pooled sequenced data obtained from such a protocol. Our algorithm employs a synergistic combination of ideas from compressed sensing and the decoding of error-correcting codes. Experimental results on synthetic data for the rice genome and real data for the barley genome show that our novel decoding algorithm enables significantly higher quality assemblies than the previous approach.
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