Accurate sample inference from amplicon data with single nucleotide resolution

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

The is mostly a wrapper tool using phyloseq and microbiome R packages.

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

Bioinformatics Pipeline

A repository with a general dada2 pipeline for amplicon processing

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

A pipeline to analyse marine fish amplicon data

A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.

R functions and workflow for submitting amplicon sequence data to the ENA.

R package for cellular DNA barcode data preprocessing.

Rsearch is an R package designed for handling and analyzing targeted sequencing data.

Mirror of amplicon-qtl repository.

Process raw Oxford Nanopore data, generate html report, and do de novo assembly (plasmid, amplicon, bacterial genome)

A series of analytical, statistical, and plotting methods in 16S rRNA gene amplicon sequencing data.