EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome
In the past decade, third-generation sequencing technologies (such as PacBio (Pacific Biosciences) and Nanopore) have become gradually matured and are widely used for microbial taxonomy and quantification. Compared with Illumina sequencing, PacBio or Nanopore has advantages with long reads and high resolution in taxonomic classification. However, there is currently a lack of an easy-to-use, reproducible, and community-supported pipeline for PacBio or Nanopore amplicon sequencing data analysis. To address this shortcoming, the highly cited EasyAmplicon is updated to version 2, a pipeline fully supporting third-generation full-length amplicon data. EasyAmplicon 2 is a user-friendly pipeline that embraces data analysis and visualization options for data obtained from various sequencing technologies (Illumina, BGI (Beijing Genomics Institution), PacBio, Nanopore or Qitan). It integrates popular tools such as DADA2 and Emu, and provides a workflow from raw data to publication-ready visualizations. EasyAmplicon 2 inherits the advantages of the previous version and further optimizes the visualization part. The updated version of the pipeline includes data preprocessing, annotation, and quantification of amplicon sequence variants, intergroup comparison, and visualization for third-generation sequencing. EasyAmplicon 2 provides a simple and easy-to-use analysis environment for long-read amplicon sequencing data analysis. It is available for free on GitHub (https://github.com/YongxinLiu/EasyAmplicon).
Authors
- Yao Wang (ORCID: https://orcid.org/0000-0001-8400-1665)
- Tong Chen (ORCID: https://orcid.org/0000-0003-3134-3113)
- Tao Wen (ORCID: https://orcid.org/0000-0003-0102-0487)
- Chuang Ma (ORCID: https://orcid.org/0000-0001-9612-7898)
- Jinrui Xun (ORCID: https://orcid.org/0000-0002-1503-1059)
- Kai Peng (ORCID: https://orcid.org/0000-0003-3256-4356)
- Xiulin Wan
- Defeng Bai (ORCID: https://orcid.org/0009-0005-7762-7199)
- Yunyun Gao (ORCID: https://orcid.org/0000-0003-3389-9385)
- Ren‐You Gan (ORCID: https://orcid.org/0000-0002-4162-1511)
- Salsabeel Yousuf
- Yang Zhou (ORCID: https://orcid.org/0000-0003-4826-7233)
- Shanshan Xu (ORCID: https://orcid.org/0000-0002-1750-4171)
- Yuanping Zhou (ORCID: https://orcid.org/0000-0002-2493-396X)
- Shi Wei Huang (ORCID: https://orcid.org/0000-0002-7529-2269)
- Xiaofang Li (ORCID: https://orcid.org/0000-0003-1554-4484)
- Baolei Jia (ORCID: https://orcid.org/0000-0001-6434-5604)
- Xia Chen (ORCID: https://orcid.org/0000-0002-7915-4568)
- Ming Zeng (ORCID: https://orcid.org/0000-0001-9717-1751)
- Yongxin Liu (ORCID: https://orcid.org/0000-0003-1832-9835)
- Tianyuan Zhang (ORCID: https://orcid.org/0000-0001-8968-563X)
- Zhihao Zhu (ORCID: https://orcid.org/0000-0001-5457-2352)
- Hao Luo (ORCID: https://orcid.org/0009-0005-3391-8576)
- Huiyu Hou
- Haifei Yang
Institutions
- Ningbo University (CN)
- Nanjing Agricultural University (CN)
- Anhui Agricultural University (CN)
- Hong Kong Polytechnic University (HK)
- Qingdao Agricultural University (CN)
- Hefei University of Technology (CN)
- Guangdong Medical College (CN)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Beijing Forestry University (CN)
- Agricultural Genomics Institute at Shenzhen (CN)
- Center for Agricultural Resources Research (CN)
- Institute of Genetics and Developmental Biology (CN)
- Chinese Academy of Agricultural Sciences (CN)
- China Academy of Chinese Medical Sciences (CN)
- Oil Crops Research Institute (CN)
- Xihu Institute of Electronic Research (CN)
- Ningbo First Hospital (CN)
- Yangzhou University (CN)
- University of Hong Kong (HK)
Publication Details
- Journal
- Advanced Science
- Published
- 2025-10-27
- DOI
- https://doi.org/10.1002/advs.202512447
- Citations
- 2
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 1.61