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

文献类型： 外文期刊

第一作者： Qiu, Zhiguang

作者： Qiu, Zhiguang;Lian, Chun-Ang;Mu, Rong;Qiao, Xuejiao;Zhang, Liyu;Ni, Jinren;Yu, Ke;Qiu, Zhiguang;Yuan, Li;Lian, Chun-Ang;Chen, Jie;Shi, Lili;Tian, Yonghong;Yu, Ke;Yuan, Li;Lin, Bin;Chen, Jie;Tian, Yonghong;Yuan, Li;Chen, Jie;Tian, Yonghong;Xu, Zheng;Xu, Zheng;Fan, Lu;Zhang, Yunzeng;Wang, Shanquan;Li, Junyi;Cao, Huiluo;Li, Bing;Chen, Baowei;Song, Chi;Song, Chi;Liu, Yongxin;Shi, Lili;Ni, Jinren;Zhang, Tong;Zhou, Jizhong;Zhuang, Wei-Qin

作者机构：

期刊名称：NATURE COMMUNICATIONS （ 影响因子：16.6； 五年影响因子：17.0 ）

ISSN：

年卷期： 2024 年 15 卷 1 期

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收录情况： SCI

摘要： 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 similar to 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.

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