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We are pleased to announce the first release of nf-core/seqsubmit, a new Nextflow pipeline that automates the submission of sequencing data — reads, metagenomic assemblies, bined contigs (bins) and metagenome-assembled genomes (MAGs) — to the European Nucleotide Archive (ENA).
We are happy to announce a new release of the MGnify Proteins database. The last release of the database in April 2024 aggregated over 2.4 billion non-redundant protein sequences generated from publicly available metagenomic datasets. This latest release more than doubles that figure, with over 5.7 billion non-redundant protein sequences now available.
We are excited to announce the release of an updated version of the MGnify Genomes marine catalogue.
This latest release (v2.0) of the marine catalogue contains data from 1628 studies, including genomes from major sampling expeditions such as Tara Oceans, Malaspina, GO-Ship, and Geotraces, amongst others.
We are thrilled to be presenting the latest MGnify Genomes catalogue comprising 112,951 genomes derived from mouse gut datasets, represented by 2,847 species-level cluster representative genomes.
MGnify is delighted to announce the release of our latest MAG catalogue, comprising 2729 species-level cluster representative genomes derived from cow rumen datasets.
MGnify are excited to announce the release of version 2 of the Unified Human Gastrointestinal Genome (UHGG) catalogue. This is an updated version of the catalogue published by Almeida et al. Nature Biotech (2021). We have added 5,878 new genomes from two studies (PRJEB37358 and PRJNA544527), representing 129 new species.
The Earth Microbiome Project is now available in MGnify. The Earth Microbiome Project (EMP)1 is a wide ranging collaborative effort that attempts to characterise the taxonomic and functional diversity of microbial life on the planet. Founded in 2010, the project includes 96 different studies, comprising approximately 26k individual sequencing runs from a diverse range of biomes.
We are pleased to announce that EBI Metagenomics has changed its name to MGnify in preparation for a series of forthcoming updates and improvements with the resource. The change also reflects the increasingly collaborative nature of the project within EMBL and across the scientific community. MGnify will continue to be a free resource for the assembly, analysis, archiving and browsing of all types of microbiome derived sequence data, providing insights into the phylogenetic diversity and functional potential of environmental samples. In addition to the new name, the website has been completely re-written to take advantage of our new API, which provides access to the metadata and analysis results.
As you may have seen from the EBI Metagenomics website, we have recently deployed a new version of our analysis pipeline (v4.1), which is now the default for analysis of submitted data. Our previous pipeline update (v4.0) was released approximately 6 months ago and involved substantial upgrades, including a move to a new method for identifying rRNAs and complete change to the way in which taxonomic analysis was performed.
This week, EBI Metagenomics hit a major milestone as we passed over one thousand publicly available projects on the site. This corresponds to over 60,000 samples, comprising more than 80,000 individual runs, and represents the analysis of over 300 billion nucleotide sequences from a wide range of environmental biomes.
The EBI Metagenomics Portal and MG-RAST are the world-leading platforms offering free-to-use analysis services for the characterisation of metagenomics sequences. The Metagenomics Exchange is a new collaboration between these platforms, aiming to promote data exchange, discovery and cross talk between the resources and their analysis pipelines. Metagenomics analysis is challenging in terms of scale of data and diversity of data.
The microbial population (or microbiome) of the human gut is involved in a wide range of important processes, such as digestion, production of vitamins and other nutrients, detoxification, protection from pathogens, and helping to shape the host immune system. Gut microbial communities represent substantial reservoirs of genetic and metabolic diversity: different people have different types of microorganisms in their gut, and community composition can change over time or with diet.
Plankton ecosystems contain a phenomenal reservoir of life: more than 10 billion organisms inhabit every litre of oceanic water, including viruses, prokaryotes, unicellular eukaryotes (protists), and metazoans.
Plankton’s importance for the earth’s climate is at least equivalent to that of the rainforest. Yet only a small fraction of organisms that compose it have been classified and analysed.