AmpSeqR: an R package for amplicon deep sequencing data analysis

https://github.com/bahlolab/AmpSeqR

AmpseqR is an R package for analysis of amplicon deep sequencing (AmpSeq) data generated on the Illumina platform. The pipeline offers various useful functions including Data pre-processing, Amplicon sequence variant (ASVs) estimation, Data post-processing, and Data visualization. Additionally, AmpseqR includes several parameters to filter noise reads and improve the accuracy of the detected haplotype.

Installation

The AmpSeqR currently available to install from Github:

# install using devtools packages
# first install devtools dependencies
if (!require(devtools)) install.packages("devtools")
devtools::install_github("bahlolab/AmpSeqR")

What data input does AmpSeqR require?

Inputs are the standard paired-end FASTQ format provided by the common Illumina sequencing platforms (e.g., MiSeq), as well as sample barcodes and target amplicon details.

Example data:

library(AmpSeqR)
example_data <- get_ampseqr_example_data()

How do I use AmpSeqR?

See the introduction vignette for usage examples.