纳米孔测序
仆从
康蒂格
纳米孔
杂交基因组组装
顺序装配
生物
计算生物学
基因组
DNA测序
转座因子
遗传学
Illumina染料测序
错误检测和纠正
DNA
计算机科学
基因
算法
纳米技术
基因表达
转录组
材料科学
作者
Sara Goodwin,James Gurtowski,Scott Ethe-Sayers,Panchajanya Deshpande,Michael C. Schatz,W. Richard McCombie
出处
期刊:Genome Research
[Cold Spring Harbor Laboratory Press]
日期:2015-10-07
卷期号:25 (11): 1750-1756
被引量:413
标识
DOI:10.1101/gr.191395.115
摘要
Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5–50 kbp) at such high error rates (between ∼5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.
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