BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis

Qiu，Zhiguang1,2; Yuan，Li2,3,4; Lian，Chun Ang1,2; Lin，Bin3; Chen，Jie2,3,4; Mu，Rong1; Qiao，Xuejiao1; Zhang，Liyu1; Xu，Zheng5,6; Fan，Lu7; Zhang，Yunzeng8; Wang，Shanquan9; Li，Junyi10; Cao，Huiluo11; Li，Bing12; Chen，Baowei13; Song，Chi14,15; Liu，Yongxin16; Shi，Lili2,17; Tian，Yonghong2,3,4; Ni，Jinren1,18; Zhang，Tong19; Zhou，Jizhong20; Zhuang，Wei Qin21; Yu，Ke1,2

2024-12-01

10.1038/s41467-024-46539-7

Nature Communications   影响因子和分区

2041-1723

Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.

SCI

英语

其他

2-s2.0-85187229469

Scopus

1.Eco-environment and Resource Efficiency Research Laboratory,School of Environment and Energy,Shenzhen Graduate School,Peking University,Shenzhen,China
2.AI for Science (AI4S)-Preferred Program,Peking University,Shenzhen,China
3.School of Electronic and Computer Engineering,Peking University,Shenzhen,China
4.Peng Cheng Laboratory,Shenzhen,China
5.Southern University of Sciences and Technology Yantian Hospital,Shenzhen,China
6.Institute of Biomedicine and Biotechnology,Shenzhen Institute of Advanced Technology,Chinese Academy of Sciences,Shenzhen,Guangdong,China
7.Department of Ocean Science and Engineering,Southern University of Science and Technology (SUSTech),Shenzhen,China
8.Joint International Research Laboratory of Agriculture and Agri-Product Safety,the Ministry of Education of China,Yangzhou University,Yangzhou,China
9.Environmental Microbiomics Research Center,School of Environmental Science and Engineering,Sun Yat-Sen University,Guangzhou,China
10.School of Computer Science and Technology,Harbin Institute of Technology (Shenzhen),Shenzhen,Guangdong,China
11.Department of Microbiology,University of Hong Kong,Hong Kong
12.Shenzhen International Graduate School,Tsinghua University,Shenzhen,China
13.Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering,School of Marine Sciences,Sun Yat-sen University,Zhuhai,China
14.Institute of Herbgenomics,Chengdu University of Traditional Chinese Medicine,Chengdu,China
15.Wuhan Benagen Technology Co.,Ltd,Wuhan,China
16.Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,China
17.State Key Laboratory of Chemical Oncogenomics,School of Chemical Biology and Biotechnology,Peking University Shenzhen Graduate School,Shenzhen,China
18.College of Environmental Sciences and Engineering,Key Laboratory of Water and Sediment Sciences,Ministry of Education,Peking University,Beijing,China
19.Department of Civil Engineering,University of Hong Kong,Hong Kong
20.Institute for Environmental Genomics,University of Oklahoma,Norman,United States
21.Department of Civil and Environmental Engineering,Faculty of Engineering,University of Auckland,Auckland,New Zealand

Qiu，Zhiguang,Yuan，Li,Lian，Chun Ang,et al. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis[J]. Nature Communications,2024,15(1).

Qiu，Zhiguang.,Yuan，Li.,Lian，Chun Ang.,Lin，Bin.,Chen，Jie.,...&Yu，Ke.(2024).BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis.Nature Communications,15(1).

Qiu，Zhiguang,et al."BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis".Nature Communications 15.1(2024).