Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis

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).

Authors

Institutions

Publication Details

Journal
iMetaOmics.
Published
2024-11-20
DOI
https://doi.org/10.1002/imo2.42
Citations
24
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
5.61

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis

Bian Bian, Tong Chen, Tao Wen, Jiao Xi et al.
24 citations
iMetaOmics.
Gut microbiota and health
5.61
article

Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis

Bian Bian, Tong Chen, Tao Wen, Jiao Xi, Xiaoya Ma, Hao Luo, Chuang Ma, Waqar Afzal Malik, Liang Chen, Jinrui Xun, Linyang Sun, Kai Peng, Tengfei Ma, Huiluo Cao, Xiulin Wan, Yunyun Gao, Ren‐You Gan, Zhicheng Ju, Hongye Lu, Maosheng Zheng, Salsabeel Yousuf, Yao Wang, Defeng Bai, Jiqiu Wu, Shanshan Xu, Yuanping Zhou, Xiaofang Li, Baolei Jia, Lei Chen, Yahui Li, Ming Zeng, Yongxin Liu, Tianyuan Zhang, Xin Zhou, Pengfan Zhang, Hujie Lyu, Shaolong Du, Huiyu Hou, Haifei Yang
article en
24 citations

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).

iMetaOmics.Vol. 1(2)
Nanjing Agricultural University (CN), University Medical Center Groningen (NL), University of Helsinki (FI), Anhui Agricultural University (CN), Hong Kong Polytechnic University (HK), Qingdao Agricultural University (CN), North China Electric Power University (CN), Hefei University of Technology (CN), University of Groningen (NL), Guangdong Medical College (CN), Capital Medical University (CN), Chinese Academy of Sciences (CN), Chinese Academy of Medical Sciences & Peking Union Medical College (CN), Hong Kong University of Science and Technology (HK), University College Cork (IE), Agricultural Genomics Institute at Shenzhen (CN), Center for Agricultural Resources Research (CN), ShenZhen People’s Hospital (CN), Innovative Genomics Institute (US), Institute of Genetics and Developmental Biology (CN), Stomatology Hospital (CN), Shenzhen Bao'an District People's Hospital (CN), Institute of Microbiology (CN), Chinese Academy of Agricultural Sciences (CN), APC Microbiome Institute (IE), China Academy of Chinese Medical Sciences (CN), Shenzhen Institutes of Advanced Technology (CN), Ministry of Agriculture and Rural Affairs (CN), Beijing Shijitan Hospital (CN), Imperial College London (GB), The University of Tokyo (JP), Zhejiang University (CN), Lanzhou University (CN), Yangzhou University (CN), University of Hong Kong (HK), Northwest A&F University (CN), University of California, Berkeley (US)
National Natural Science Foundation of China, China Postdoctoral Science Foundation, Chinese Academy of Agricultural Sciences, Agricultural Science and Technology Innovation Program
Openalex Percentile: Top 3%
Gut microbiota and health
5.61
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.