EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research
Agricultural Genomics Institute at Shenzhen · Chinese Academy of Agricultural Sciences · +33 more institutions
Abstract
It is difficult for beginners to learn and use amplicon analysis software because there are so many software tools to choose from, and all of them need multiple steps of operation. Herein, we provide a cross-platform, open-source, and community-supported analysis pipeline EasyAmplicon. EasyAmplicon has most of the modules needed for an amplicon analysis, including data quality control, merging of paired-end reads, dereplication, clustering or denoising, chimera detection, generation of feature tables, taxonomic diversity analysis, compositional analysis, biomarker discovery, and publication-quality visualization. EasyAmplicon includes more than 30 cross-platform modules and R packages commonly used in the…
Citation impact
- FWCI
- 38.29
- Percentile
- 100%
- References
- 62
Authors
22- YLYongxin LiuCorresponding
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs
- LCLei Chen
Capital Medical University, Chinese Academy of Sciences, Institute of Microbiology
- TMTengfei Ma
Gansu Agricultural University, Ministry of Agriculture, Lanzhou University
- XLXiaofang Li
Chinese Academy of Sciences, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology
- MZMaosheng Zheng
North China Electric Power University
Topics & keywords
- Amplicon
- Pipeline (software)
- Microbiome
- Open source
- Data science
- Computer science
- Computational biology
- Biology