MGnify (formerly known as EBI Metagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data.

MGnify is EMBL-EBI's metagenomics resource. EMBL-EBI are one of the 11 HoloFood partners, and are responsible for the analysis of metagenomic and microbial datasets from the project.

CWL-assembly

Description

This repository contains two workflows for metagenome and ...

EukRecover

Pipeline to recover eukaryotic MAGs using CONCOCT, metaBAT2 and EukCC's merging algorythm.

Needs paired end shotgun metagenomic reads.

Environment

Eukrecover requires an environment with snakemake and metaWRAP.

Quickstart

Define your samples in the file samples.csv. This file needs to have the columns project and run to identify each metagenome.

This pipeline does not support co-binning, but feel free to change it.

Clone this repro wherever you want to run the pipeline:

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Assembly and quantification metatranscriptome using metagenome data.

Version: see VERSION

Introduction

MetaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by ...

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...