tidyGenR: Tidy multilocus amplicon genotypes in R

R package optimized for genotyping multilocus amplicon sequences from High Throughput Sequencing. Starting with FASTQ multilocus amplicon sequencing reads from high throughput sequencing, it demultiplexes reads by locus, call variants (using DADA2), and genotypes samples. It generates tidy variants and genotypes outputs, and it provides a family of functions for data manipulation and format conversion.

Installation

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
# remotes::install_github("csmiguel/tidyGenR")
install.packages("tidyGenR", repos = c('https://csmiguel.r-universe.dev', 'https://cloud.r-project.org'))
# or install .tar.gz:
# remotes::install_local("tidyGenR-x.x.x.tar.gz", dependencies = TRUE, build_vignettes = TRUE)

Workflow

The main worflow is avaible in vignette("tidyGenR-intro", "tidyGenR"). Deeper explanations together with benchmarking and extra funcionalities are available in tidyGenR_benchmarking repository and deployed webpage.