Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing.
Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing.
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DOI：
10.1186/s13059-021-02282-6
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发表时间：
2021-03-31
期刊：
影响因子：
12.3
通讯作者：
Shih PW
中科院分区：
文献类型：
--
作者：
Huang YT;Liu PY;Shih PW
纳米孔测序已被广泛应用于微生物基因组的重建。由于更高的错误率，基因组上的错误通过Nanopore Reads训练的神经网络得到纠正。然而，系统误差通常仍未得到纠正。本文设计了一种由同源序列训练的纳米孔系统误差校正模型。开发的程序Homopolish在细菌、病毒、真菌和元基因组数据集方面优于Medaka和Helen。当与Medaka/Helen结合时，R9.4 Flow细胞的基因组质量可以超过Q50。我们证明，只有纳米孔测序可以产生高质量的微生物基因组，足以进行下游分析。网上版载有补充材料，可在(10.1186/s13059-021-02282-6)查阅。
Nanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. This paper designs a model that is trained by homologous sequences for the correction of Nanopore systematic errors. The developed program, Homopolish, outperforms Medaka and HELEN in bacteria, viruses, fungi, and metagenomic datasets. When combined with Medaka/HELEN, the genome quality can exceed Q50 on R9.4 flow cells. We show that Nanopore-only sequencing can produce high-quality microbial genomes sufficient for downstream analysis. The online version contains supplementary material available at (10.1186/s13059-021-02282-6).
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