HoloFood is a 'hologenomic' approach that will improve the efficiency of food production systems by understanding the biomolecular and physiological processes affected by incorporating feed additives and novel sustainable feeds in farmed animals.
The HoloFood consortium will showcase the potential of an innovative solution that holds enormous potential for optimising modern food production. Specifically, HoloFood is a framework that integrates a suite of recent analytical and technological ...
Teams: HoloFood at MGnify
Web page: https://www.holofood.eu
MGnify (formerly known as EBI Metagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data.
Space: This Team is not associated with a Space
Public web page: https://www.ebi.ac.uk/metagenomics/
Organisms: Not specified
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.
Authors: Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski
Date Published: 28th Oct 2022
Publication Type: Journal
Citation: Front. Microbiol. 13,981458
Pipeline to recover eukaryotic MAGs using CONCOCT, metaBAT2 and EukCC's merging algorythm.
Needs paired end shotgun metagenomic reads.
Eukrecover requires an environment with snakemake and metaWRAP.
Define your samples in the file
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:
Submitter: Varsha Kale
Assembly and quantification metatranscriptome using metagenome data.
Version: see VERSION
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 ...
Type: Common Workflow Language
Creators: Ekaterina Sakharova, Varsha Kale, Martin Beracochea, Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea