Fast and accurate de novo genome assembly from long uncorrected reads

Fast and accurate de novo genome assembly from long uncorrected reads

快速和准确的从头基因组组装从长时间未纠正的read

1. Robert Vaser1,5, 
2. Ivan Sović2,5, 
3. Niranjan Nagarajan3 and 
4. Mile Šikić1,4

+Author Affiliations

1. ¹Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, 10000 Zagreb, Croatia;
2. ²Centre for Informatics and Computing, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
3. ³Genome Institute of Singapore, Singapore 138672, Singapore;
4. ⁴Bioinformatics Institute, Singapore 138671, Singapore

1. Corresponding author: mile.sikic@fer.hr

1. ↵5 These authors contributed equally to this work.

Abstract

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment–based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

太平洋生物科学公司和牛津纳米孔技术公司的长片段组装通常需要资源密集型的纠错和共识生成步骤，以获得高质量的组装。
我们的研究表明，使用名为Racon的simd加速、基于部分顺序对齐的独立的consensus模块，可以省去错误校正步骤，并有效地生成高质量的consensus序列。
基于对PacBio和Oxford Nanopore数据集的测试，我们发现，Racon与miniasm相结合可以实现与最先进的方法相似或更好的一致基因组，同时速度更快一个数量级。