metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies

Senying Lai; Shaojun Pan; Chuqing Sun; Luis Pedro Coelho; Wei-Hua Chen; Xing-Ming Zhao

doi:10.1186/s13059-022-02810-y

metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies

Genome Biol. 2022 Nov 14;23(1):242. doi: 10.1186/s13059-022-02810-y.

Authors

Senying Lai¹, Shaojun Pan¹, Chuqing Sun², Luis Pedro Coelho^{3

4}, Wei-Hua Chen^{5

6}, Xing-Ming Zhao^{7

8

9

10

11

12}

Affiliations

¹ Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
² Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
³ Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. luis@luispedro.org.
⁴ MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China. luis@luispedro.org.
⁵ Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China. weihuachen@hust.edu.cn.
⁶ College of Life Science, Henan Normal University, Xinxiang, Henan, China. weihuachen@hust.edu.cn.
⁷ Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
⁸ MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
⁹ State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
¹⁰ Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China. xmzhao@fudan.edu.cn.
¹¹ International Human Phenome Institutes (Shanghai), Shanghai, China. xmzhao@fudan.edu.cn.
¹² Zhangjiang Fudan International Innovation Center, Shanghai, China. xmzhao@fudan.edu.cn.

Abstract

Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC ( https://github.com/ZhaoXM-Lab/metaMIC ), a machine learning-based tool for identifying and correcting misassemblies in metagenomic assemblies. Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.

Keywords: Binning; Metagenome-assembled genomes; Metagenomic assemblies; Misassembled contigs; Misassembly breakpoints.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Benchmarking
Machine Learning
Metagenome*
Metagenomics* / methods
Sequence Analysis, DNA / methods
Software