Highly accurate-single chromosomal complete genomes using IonTorrent and MinION sequencing of clinical pathogens
Highly accurate-single chromosomal complete genomes using IonTorrent and MinION sequencing of clinical pathogens
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DOI：
10.1016/j.ygeno.2019.04.006
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发表时间：
2020-01-01
期刊：
影响因子：
4.4
通讯作者：
Veeraraghavan, Balaji
中科院分区：
文献类型：
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作者：
Vasudevan, Karthick;Ragupathi, Naveen Kumar Devanga;Veeraraghavan, Balaji
Oxford Nanopore MinION测序技术在鉴定病原体和抗微生物药物耐药性方面具有巨大的重要性，尽管错误率为10-15%。短读技术产生高准确度的基因组，但具有多个基因组片段。本研究提出了一种新的工作流程，通过在临床分离株中覆盖来自IonTorrent的短读段序列来减少MinION长读段测序导致的插入缺失。利用这两种技术中的最佳技术，产生了高度准确的单染色体微生物基因组，其中铜绿假单胞菌、A. veronii和B.百日咳分别。据我们所知，这是第一项产生IonTorrent和MinION读数的混合物以获得单染色体基因组的研究。这将使得能够精确地推断基因的结构排列和基于SNP的系统发育信息分析。
Oxford Nanopore MinION sequencing technology has been gaining immense importance in identification of pathogen and antimicrobial resistance, though with 10-15% error rate. Short read technologies generates high accurate genome but with multiple fragments of genome. This study proposes a novel workflow to reduce the indels resulted from MinION long read sequencing by overlaying short read sequences from IonTorrent in the clinical isolates. Best of both techniques were employed which generated highly accurate-single chromosomal microbial genomes with increase in completeness of genomes from 44.5%, 30% and 43% to 98.6%, 98.6% and 96.6% for P. aeruginosa, A. veronii and B. pertussis respectively. To the best of our knowledge, this is the first study to generate a hybrid of IonTorrent and MinION reads to obtain single chromosomal genomes. This would enable to precisely infer both structural arrangement of genes and SNP based analysis for phylogenetic information.