The Flexible Demultiplexer

Open-source usearch

A quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences

The CoastMon repository contains scripts for metagenomics/metatranscriptomics analysis of eDNA samples for coastal monitoring purposes.

Plotting scripts for long read sequencing data

Oxford Nanopore's Basecaller

Tools for visualising microbial community amplicon data

Microbiome classification pipeline

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Differential abundance (DA) and correlation analyses for microbial absolute abundance data

QIIME2 and R scripts, 16S sequencing pipeline and analysis

Gephi - The Open Graph Viz Platform

A minimal book example using bookdown

PASTA (Practical Alignment using SATe and Transitivity)