Journal
NATURE COMMUNICATIONS
Volume 12, Issue 1, Pages -Publisher
NATURE RESEARCH
DOI: 10.1038/s41467-020-20236-7
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Funding
- National Natural Science Foundation of China [31871326, 31701146, 91953122, 61732009, U1909208, 81530028, 81721003]
- Guangdong Basic and Applied Basic Research Foundation [2020B1515020057]
- Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program
- CAMS Innovation Fund for Medical Sciences [2019-I2M-5-005]
- Clinical Innovation Research Program of Guangzhou Regenerative Medicine and Health Guangdong Laboratory [2018GZR0201001]
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University
- US National Institute of Food and Agriculture (NIFA) [2017-70016-26051]
- US National Science Foundation (NSF) [ABI-1759856]
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The error correction and de novo assembly tool NECAT developed by the authors efficiently produces high-quality assemblies of nanopore reads. The tool utilizes adaptive read selection and a two-step progressive method to overcome the high error rates in nanopore reads.
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection. Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads.
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