De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
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DOI：
10.1105/tpc.17.00521
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发表时间：
2017-10-01
期刊：
影响因子：
11.6
通讯作者：
Usadel, Bjorn
中科院分区：
文献类型：
--
作者：
Schmidt, Maximilian H. -W.;Vogel, Alexander;Usadel, Bjorn
纳米孔技术的更新使得获得千兆字节的序列数据成为可能。在此之前，纳米孔测序技术主要用于分析微生物样品。在这里，我们描述了一个全面的纳米孔测序数据集的产生，具有11，979 bp的中值读取长度的野生番茄物种的自相容的加入。我们将其基因组组装成2.5 MB的重叠群N50。组装管道包括Canu的初始读取校正和SMARTdenovo的组装。所得的基于纳米孔的原始从头基因组在结构上与参比S. pennellii LA716登录，但具有高错误率且富含同聚物缺失。在使用Illumina读取对组装进行抛光后，我们获得了错误率为
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of