Table 1.
Software and packages included in EasyAmplicon
| Software | Function in the pipeline | Website |
|---|---|---|
| Git for Windows | Provides Linux Shell like environment in Windows | http://gitforwindows.org/ |
| R | Statistical processing and data visualization | https://www.r-project.org |
| RStudio | Integrated development environment for R and Shell | https://posit.co/ |
| VSEARCH | A fast, free, and cross‐platform pipeline for amplicon sequencing analysis [34] | https://github.com/torognes/vsearch |
| USEARCH | Processes sequences and calculates alpha‐ and beta‐diversities [19] | http://www.drive5.com/usearch/ |
| SeqKit | Toolkit for FASTA or FASTQ file manipulation [35] | https://github.com/shenwei356/seqkit |
| ggplot2 | R package for data visualization | https://github.com/tidyverse/ggplot2 |
| ggClusterNet | R package for microbiome network visualization [36] | https://github.com/taowenmicro/ggClusterNet/ |
| vegan | R package for alpha and beta diversity analysis | https://cran.r-project.org/package=vegan |
| ggraph | Creates layout for tree map and circle packing chart | https://github.com/thomasp85/ggraph |
| circlize | Circular visualization [37] | https://github.com/jokergoo/circlize |