Metagenomics toolkit

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Python script Need to compile metadata to perform trait associations using our metagenomic data? Interested in correlating species abundance with the origin of the sample to identify organisms associated with a particular environment or state? Try our latest metagenomics toolkit (called: “mg-toolkit”) - a beta version of a tool to enable scientists to download all of the sample metadata for a given study to a single csv file. Simply install as follows:

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Metagenomics rest api

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Python script Want to perform comprehensive meta-analysis of samples from publicly available metagenomics studies? Interested in discovering patterns in metagenomic data to predict disease? Our REST API allows both human and machines to query over 100,000 publicly available metagenomic and metatranscriptomic datasets. The base URL to the API https://www.ebi.ac.uk/metagenomics/api/ provides access to several data collections, such as studies, samples, runs, biomes and experiment-types. They can be filtered by a set of attributes, such as biome, allowing selection of samples that belong to the same microbial ecosystem. For instance, to retrieve oceanic data: https://www.ebi.ac.uk/metagenomics/api/latest/studies?lineage=root%3AEnvironmental%3AAquatic%3AMarine%3AOceanic. Retrieving data from our API is as simple as sending an HTTP request, where the response returns a JSON object formatted data structure that contains the resource type, associated object identifier (id) with attributes and relationships linking to other resources. For example, https://www.ebi.ac.uk/metagenomics/api/latest/studies/PRJEB1787 retrieves a metagenomics dataset produced during experiments of the Tara Oceans Expedition.

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Pipeline release version 4.1

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Analysis Pipeline v4.1 Released

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.

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A major milestone

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One Thousand Publicly Available Projects

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.

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Bulk download

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Python script Interested in bulk download of our data? Did you know that we provide a Python script for the bulk download of publicly available project data? The tool iterates over all samples and runs in a project and builds an appropriate root URL, which it uses to download individual run result files. Different file types can be specified, allowing you to download, for example, all reads encoding 16S rRNAs, all taxonomic assignments, or all predicted protein coding sequences, for a particular project. To find out more, click the ‘Bulk download script’ link below.

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Software developer position

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We are hiring!

Job alert 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.

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Functional sample comparison

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Functional sample comparison Interested in comparing the functional profile of sequencing runs within a project? Now it is possible, using our comparison tool, which provides analysis based on a slimmed-down subset of Gene Ontology (GO) terms, specially developed to describe metagenomic data.

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American Gut project

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American Gut project 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.

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TARA oceans project

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Tara oceans project map 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.

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