Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis
Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for...
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Wiley
2024-12-01
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| Series: | iMetaOmics |
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| Online Access: | https://doi.org/10.1002/imo2.42 |
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| author | Salsabeel Yousuf Hao Luo Meiyin Zeng Lei Chen Tengfei Ma Xiaofang Li Maosheng Zheng Xin Zhou Liang Chen Jiao Xi Hongye Lu Huiluo Cao Xiaoya Ma Bian Bian Pengfan Zhang Jiqiu Wu Renyou Gan Baolei Jia Linyang Sun Zhicheng Ju Yunyun Gao Waqar Afzal Malik Chuang Ma Hujie Lyu Yahui Li Huiyu Hou Yuanping Zhou Defeng Bai Yao Wang Haifei Yang Jiani Xun Shengda Du Tianyuan Zhang Xiulin Wan Kai Peng Shanshan Xu Tao Wen Tong Chen Yong‐Xin Liu |
| author_facet | Salsabeel Yousuf Hao Luo Meiyin Zeng Lei Chen Tengfei Ma Xiaofang Li Maosheng Zheng Xin Zhou Liang Chen Jiao Xi Hongye Lu Huiluo Cao Xiaoya Ma Bian Bian Pengfan Zhang Jiqiu Wu Renyou Gan Baolei Jia Linyang Sun Zhicheng Ju Yunyun Gao Waqar Afzal Malik Chuang Ma Hujie Lyu Yahui Li Huiyu Hou Yuanping Zhou Defeng Bai Yao Wang Haifei Yang Jiani Xun Shengda Du Tianyuan Zhang Xiulin Wan Kai Peng Shanshan Xu Tao Wen Tong Chen Yong‐Xin Liu |
| author_sort | Salsabeel Yousuf |
| collection | DOAJ |
| description | Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user‐friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon). |
| format | Article |
| id | doaj-art-1aec4e513b4648ff99ab97432c63186d |
| institution | Kabale University |
| issn | 2996-9506 2996-9514 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | iMetaOmics |
| spelling | doaj-art-1aec4e513b4648ff99ab97432c63186d2025-01-31T16:15:24ZengWileyiMetaOmics2996-95062996-95142024-12-0112n/an/a10.1002/imo2.42Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysisSalsabeel Yousuf0Hao Luo1Meiyin Zeng2Lei Chen3Tengfei Ma4Xiaofang Li5Maosheng Zheng6Xin Zhou7Liang Chen8Jiao Xi9Hongye Lu10Huiluo Cao11Xiaoya Ma12Bian Bian13Pengfan Zhang14Jiqiu Wu15Renyou Gan16Baolei Jia17Linyang Sun18Zhicheng Ju19Yunyun Gao20Waqar Afzal Malik21Chuang Ma22Hujie Lyu23Yahui Li24Huiyu Hou25Yuanping Zhou26Defeng Bai27Yao Wang28Haifei Yang29Jiani Xun30Shengda Du31Tianyuan Zhang32Xiulin Wan33Kai Peng34Shanshan Xu35Tao Wen36Tong Chen37Yong‐Xin Liu38Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaDepartment of Vascular Surgery, Fu Xing Hospital Capital Medical University Beijing ChinaState Key Laboratory of Herbage Improvement and Grassland Agro‐Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology Lanzhou University Lanzhou Gansu ChinaCentre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences Shijiazhuang Hebei ChinaCollege of Environmental Science and Engineering North China Electric Power University Beijing ChinaState Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences Beijing ChinaBiomedical Innovation Center and Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital Capital Medical University Beijing ChinaCollege of Natural Resources and Environment Northwest A&F University Yangling Shaanxi ChinaStomatology Hospital, School of Stomatology Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province Hangzhou Zhejiang ChinaDepartment of Microbiology University of Hong Kong Pok Fu Lam Hong Kong ChinaCenter for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen Guangdong ChinaDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences The University of Tokyo Kashiwa, Chiba JapanInnovative Genomics Institute University of California Berkeley California USAAPC Microbiome Institute University College Cork Cork IrelandDepartment of Food Science and Nutrition, Faculty of Science The Hong Kong Polytechnic University Kowloon Hong Kong ChinaXianghu Laboratory Hangzhou Zhejiang ChinaFaculty of Biological & Environmental Sciences University of Helsinki Helsinki FinlandDepartment of Ocean Science The Hong Kong University of Science and Technology Clear Water Bay Hongkong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaDepartment of Life Sciences, Imperial College of London London UKGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaJiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University Yangzhou Jiangsu ChinaSchool of Food and Biological Engineering Hefei University of Technology Hefei Anhui ChinaJiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic‐Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource‐Saving Fertilizers Nanjing Agricultural University Nanjing Jiangsu ChinaState Key Laboratory for Quality Assurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing ChinaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong ChinaAbstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user‐friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon).https://doi.org/10.1002/imo2.42computational biologyEasyAmpliconmetagenomemicrobiome |
| spellingShingle | Salsabeel Yousuf Hao Luo Meiyin Zeng Lei Chen Tengfei Ma Xiaofang Li Maosheng Zheng Xin Zhou Liang Chen Jiao Xi Hongye Lu Huiluo Cao Xiaoya Ma Bian Bian Pengfan Zhang Jiqiu Wu Renyou Gan Baolei Jia Linyang Sun Zhicheng Ju Yunyun Gao Waqar Afzal Malik Chuang Ma Hujie Lyu Yahui Li Huiyu Hou Yuanping Zhou Defeng Bai Yao Wang Haifei Yang Jiani Xun Shengda Du Tianyuan Zhang Xiulin Wan Kai Peng Shanshan Xu Tao Wen Tong Chen Yong‐Xin Liu Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis iMetaOmics computational biology EasyAmplicon metagenome microbiome |
| title | Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis |
| title_full | Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis |
| title_fullStr | Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis |
| title_full_unstemmed | Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis |
| title_short | Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis |
| title_sort | unveiling microbial communities with easyamplicon a user centric guide to perform amplicon sequencing data analysis |
| topic | computational biology EasyAmplicon metagenome microbiome |
| url | https://doi.org/10.1002/imo2.42 |
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