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.

Support and Contact

AmpSeqR is actively maintained.
If you encounter any issues or have questions, please open an issue on GitHub
or email us: Jiru Han (han.ji@wehi.edu.au)