Metagenomic binning based on Hi-C data

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

A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.

MGKit: Metagenomics Framework

MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards

A metagenome assembly and evaluation pipeline, focused on hi-fi long reads, but with support for lo-fi long reads and hybrid assemblies

🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean

Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.

KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.

:horse: CLinically Okay Metagenomic Pipeline :horse:

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline

MetaBolt: Lightning fast & automated metagenomic pipeline powered by Nextflow

quantify-virome: identify and quantify viruses from metagenomic shotgun sequences

🗂️Parse multiple Kraken2 reports into CSV files on 6 taxonomical levels

A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis

The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.

Metagenomic analysis of the project: "Metabolic programmimg for resilience small litter size preserves gut microbiota diversity and SCFA output despite high-sucrose diet"

Projeto de análise metagenômica e metabolômica da microbiota de mulheres no climatério - LBBM UFOP

iMAGine - In silico Metagenomics Pipeline

宏基因组预测

WGS- Metasociomic- analysing bacterial social interactions in metagenomes of longitudinally collected samples of human microbiomes

This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

Milk Metagenomics Analysis of Cow Milk Samples across Global sites Using Mothur

This is a metagenomics pipeline to detect phages and Auxiliary Metabolic Genes (AMGs) from specific virtual genomes of bacteria (MAGs) in the human microbiome.

MAPle provides three different modules for the analysis of paired-end short read metagenomic data

ConsensusMetaDA is an R package that runs five popular metagenomic differential abundance algorithms

MegaVir is a bioinformatic pipeline for virome characterization and genome assembly.

Simple Script for Metagenomics Analysis on NIG Supercomputer (National Institute of Genetics)

Oral Microbiome & Metagenomic analysis for the Characterization of a uSGB