Amplicon sequencing analysis workflow using DADA2 and QIIME2

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Tools for visualising microbial community amplicon data

In-silico PCR, primer design and padlock design for in-situ sequencing

Various functions for analysis of microbial community data

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

microhaplotype visualizer and analyzer

Metagenomics calibration R package

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

gNOMO2 allows integrated multi-omics analyses of microbiomes

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package

A web app for environmental DNA metabarcoding analysis

SCRAPT: An Iterative Algorithm for Clustering Large 16S rRNA Gene Datasets

Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data