Skip to content
Branch: master
Find file History
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
..
Failed to load latest commit information.
MGnify-presentation.pdf
README.md

README.md

Enrichment and propagation of metagenomic experimental metadata.

### Representative: Ola Tarkowska

Community


Elixir Marine Metagenomics Community, Data clearing warehouse IS and Interoperability Platform

Leads


Maxim Sheremetjew, Ola Tarkowska, Miguel Boland

Background information


The use of marker gene amplification (e.g. SSU rRNA) is widespread in metagenomics, providing insights to the microbes that are present within a biome. However, the primers and/or targeted variable region is often lacking (or mislabelled) in the metadata associated with the deposited sequence record. Resources such as MGnify, are dependent on this data when trying to compare datasets as different experimental methods introduce nuisance variables into statistical analyses. We propose the development of a new tool to infer the SSU rRNA variable region based on the analysed sequence data in MGnify. Thereafter, will also develop workflows to propagate the metadata (including inference method) to relevant resources.

Expected outcomes


New tool to infer amplified SSU rRNA variable region, based on sequence analysis by MGnify, and pipeline to push this data to the various archiving resources, such as ENA and BioSamples. Integrating the new tool within MGnify API will help harmonise data and improve exchange between resources.

Expected audience


Representatives from the service providers, such as ENA and BioSamples, who will help with structuring, propagating and harmonising the enriched metadata to their resources. Expected hacking days: 3 days

Related works and references


https://en.wikipedia.org/wiki/SSU_rRNA https://en.wikipedia.org/wiki/Hypervariable_region https://www.ebi.ac.uk/metagenomics/

GitHub or any other public repositories of your FOSS products (if any)


https://github.com/EBI-Metagenomics/emg-toolkit https://github.com/EBI-Metagenomics/emgapi

Hackers


Achivements


Script infering variable regions from MGnify analysis results is avaialble on https://github.com/EBI-Metagenomics/elixir-biohackathon MGnify API changes are avaible in https://github.com/EBI-Metagenomics/emgapi/tree/biohackathon

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.