纳米孔测序
计算机科学
顺序装配
生物
参考基因组
DNA测序
杂交基因组组装
软件
基因组
计算生物学
遗传学
基因
DNA
基因表达
转录组
程序设计语言
作者
Valentine Murigneux,Subash Kumar,Agnelo Furtado,Timothy J. C. Bruxner,Wei Tian,Ivon Harliwong,Hanmin Wei,Bicheng Yang,Qianyu Ye,Ellis Anderson,Qing Mao,Radoje Drmanac,Ou Wang,Brock A. Peters,Mengyang Xu,Pei‐Ju Wu,Bruce Topp,Lachlan Coin,Robert J. Henry
出处
期刊:GigaScience
[Oxford University Press]
日期:2020-12-01
卷期号:9 (12)
被引量:62
标识
DOI:10.1093/gigascience/giaa146
摘要
Abstract Background Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. Results Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. Conclusions The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
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