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phac-nml / irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
https://irida.ca
Apache License 2.0
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Metadata should be automatically populated with sequencing platform and serial number #817

Open dorbarker opened 3 years ago

dorbarker commented 3 years ago

Describe your idea for a new feature

Metadata would be automatically populated with the sequencer instrument model. Ideally, the sequencer's serial number (or other identifier) would also be included.

This would move more essential information about sequence data to IRIDA (and out of random Excel sheets, one hopes). Recording the serial number would be helpful if it's later found that there was a problem with that particular device, e.g. identifying samples that would need to be re-sequenced.

Describe how you would access this feature?

Sequencer instrument model and serial number would be automatically generated fields available in Line List.

Sample Modified Date Created Date Instrument Model Instrument Serial Number
foo Oct 5, 2020 5:53 PM Oct 5, 2020 6:00 PM Illumina NextSeq 550 1234567890

Additional information

Related to #802 Likely to involve phac-nml/irida-uploader

tom114 commented 3 years ago

Thanks @dorbarker I like the idea, or something similar to this anyway. You're right it would likely involve the uploader project, could potentially be added from there without any changes to IRIDA itself.

dorbarker commented 3 years ago

My wet-lab colleagues also consider the reagent kit and flowcell ID and lot numbers also important for the same reasons. I don't know if the sequencers make this information available to irida-uploader, though. If it is, it would definitely have big benefits for QA and just general data organizing.

tom114 commented 3 years ago

Thanks @dorbarker. I suspect something like this wouldn't be done for the whole system, but maybe configurable somehow per lab, project, etc. We've been doing some scripting with the uploader codebase to manage metadata in IRIDA, so something along those lines might make sense. In that way it may not even need directly tied to the uploader, but some other related scripting. We'll leave this open for discussion for now even if it doesn't apply directly to this github project.