MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Chuan-Le Xiao; Ying Chen; Shang-Qian Xie; Kai-Ning Chen; Yan Wang; Yue Han; Feng Luo; Zhi Xie

doi:10.1038/nmeth.4432

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Nat Methods. 2017 Nov;14(11):1072-1074. doi: 10.1038/nmeth.4432. Epub 2017 Sep 18.

Authors

Chuan-Le Xiao^{1

2

3

4}, Ying Chen², Shang-Qian Xie^{1

5}, Kai-Ning Chen¹, Yan Wang¹, Yue Han^{1

6}, Feng Luo⁷, Zhi Xie¹

Affiliations

¹ State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
² School of Data and Computer Science, and Guangdong Provincial Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou, China.
³ Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Hunan, China.
⁴ College of Plant Protection, Hunan Agricultural University, Changsha, China.
⁵ Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.
⁶ CookGene Bio-technology Co., Ltd., Guangzhou, China.
⁷ School of Computing, Clemson University, Clemson, South Carolina, USA.

PMID: 28945707
DOI: 10.1038/nmeth.4432

Abstract

We present a tool that combines fast mapping, error correction, and de novo assembly (MECAT; accessible at https://github.com/xiaochuanle/MECAT) for processing single-molecule sequencing (SMS) reads. MECAT's computing efficiency is superior to that of current tools, while the results MECAT produces are comparable or improved. MECAT enables reference mapping or de novo assembly of large genomes using SMS reads on a single computer.

MeSH terms

Algorithms
High-Throughput Nucleotide Sequencing / methods*
Sequence Analysis, DNA / methods*
Software