Can I run the EBI metagenomics pipeline locally?

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6.7 years ago

alesssia ▴ 580

Hello everyone,

I was wondering whether the EBI metagenomics pipeline ( https://www.ebi.ac.uk/metagenomics/ ) could be run locally. Here https://emg-docs.readthedocs.io/en/latest/_images/pipeline_v4.1b_overview.png there is an overview of the processing flow which specifies the software used and some parameters, but I am wondering whether all the set parameters are listed, and whether the queried databases are available for download.

I am interested in comparing it with a few other metagenomics pipelines using a set of simulated datasets, and I would avoid uploading them and wait for the EBI/ENA checks.

Thanks a lot!

metagenomics pipeline EBI • 1.3k views

ADD COMMENT • link updated 6.7 years ago by h.mon 35k • written 6.7 years ago by alesssia ▴ 580

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Entering edit mode

May be best submitted to EBI help desk.

Will tag Emily_Ensembl in case she has an input.

ADD REPLY • link 6.7 years ago by GenoMax 148k

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