A collection of Galaxy-related training material

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

Detecting contamination in NGS data and multi-species analysis

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

An interactive radial tree for functional hierarchies and omics data visualization

Integrated Machine Learning for Multi-omics Classification and Prediction

Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bioinformatics/btac389

Open-source opinionated Galaxy-based framework for microbiota analysis

💯 Snakemake-based amplicon processing protocol for 16S and ITS sequences.

Searching large collections of sequencing data with genome-scale queries

🍰 Per sequence functional classification and taxonomic assignments

Pipeline to pull microbial reads from WGS data and perform metagenomic analysis

Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators

Ancient DNA Read Simulator for Metagenomic

MetaTrinity is a novel metagenomic analysis tool employing efficient containment search techniques and heuristics for read mapping to achieve significant speedup while maintaining high accuracy. This positions MetaTrinity as an efficient solution, optimally balancing speed and precision in metagenomic analysis.

How to analyze shotgun metagenomic data with phyloseq - a walkthrough

Collection of walkthrough tutorials on how to use Tweedieverse for differential analysis of omics data.

A metagenome annotation workflow for UBC's Microbiology 405 course, Bioinformatics

A knowledge graph of the wastewater treatment microbiome and its biological context

Microbiome Study of Lupus Patients