Hao Luo, Defeng Bai, Zhihao Zhu, Salsabeel Yousuf, Haifei Yang, Jinrui Xun, Meiyin Zeng, Yao Wang, Yunyun Gao, Kai Peng, Shanshan Xu, Yuanping Zhou, Tianyuan Zhang, Chuang Ma, Huiyu Hou, Xiulin Wan, Yang Zhou, Baolei Jia, Shi Huang, Ren‐You Gan, Tao Wen, Tong Chen, Xia Chen, Xiaofang Li, Yongxin Liu
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).