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

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

metagenome simulation for targeted and reduced-representation sequencing

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

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

NanoASV official repo

Amplicon sequencing analysis workflow using DADA2 and QIIME2

short-read amplicon data visualization suite

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

Workflow and R scripts for Giongo et al. (2024)

This pipeline reconstructs the composition of species from 16S amplicon sequencing datasets.

A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods

MicrobioSee2, a desktop sofware for visulization of microbiome result, which contian multiple modules, such as Alpha Diversity, Beta Diversity, Species Conpositions, volcano plot, and pie chart.

A state-of-the-art snakemake workflow for amplicon sequencing

Microbial Community Analysis with Chipster

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

𝐛𝐚𝐫𝐛𝐚𝐜 is an R package designed for the 𝘦𝘹𝘵𝘳𝘢𝘤𝘵𝘪𝘰𝘯 of barcode sequences. It efficiently 𝘤𝘭𝘶𝘴𝘵𝘦𝘳𝘴 these sequences and provides functionality for the calculation and visualization of 𝘵𝘪𝘮𝘦 𝘴𝘦𝘳𝘪𝘦𝘴 trajectories of the barcoded data.

Tools for visualising microbial community amplicon data

Tesis licenciatura "Metataxonómica de bacterias comoindicador de la descarga de xenobióticos por el Anillo de Cenotes en el sedimento de manglar rojo"

Docs for AmpliPiper, developed by @nhmvienna