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NorwegianVeterinaryInstitute / DemultiplexRawSequenceData

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to archiving and processing afterwards
GNU General Public License v3.0
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discussion: 221124_M06578_0124_000000000-KNW3P Sample_Project name: 12160-123-ringtest ? #66

Closed georgemarselis-nvi closed 1 year ago

georgemarselis-nvi commented 1 year ago

I was testing the new demultiplexing script at work with run 221124_M06578_0124_000000000-KNW3P

and this project name came up: 12160-123-ringtest image

I asked Magnus about it and he said "Ringtest is sample material being sent to several labs to compare results. This is linked to accreditation of methods" but he does not know the details.

The question here is two steps:

  1. Can we have a max 2 paragraph write up on what it is
  2. Do we treat it as a control run? do we treat it as a regular run? or is it another case we need to take care of while demultiplexing?

to be discussed.

karinlag commented 1 year ago
  1. Ring trials: @01schau, can you say if I am mistaken or not in what I say below?

Norway is a member state of EFSA, which is the European Food Authority in many ways. They run tests to enable laboratories in the member states to see whether their methods work correctly or not. They send out samples (or data) to the member state laboratories. We are one such lab. We then do what we do to figure out what they are testing for, and then we submit our results to them. They then let us know how we did. So, think of it as benchmarking our methods, if you will.

  1. These should most definitively go in VIGAS, i.e. a regular run. We need to get to the point where we add metadata at some point, so we can know that these are ring trial samples, but that is for later.
georgemarselis-nvi commented 1 year ago

2. These should most definitively go in VIGAS, i.e. a regular run. We need to get to the point where we add metadata at some point, so we can know that these are ring trial samples, but that is for later.

can we discuss if or how we need to tag them in the demultiplexing script? i'd rather not have to circle back to tag these manually later.

karinlag commented 1 year ago

They are not tagged in any way in the demultiplex script. They will be tagged in Clarity and via that way into the sample sheet, so for the demultiplex script it won't be any different.

georgemarselis-nvi commented 1 year ago

i meant to say, "in that case, i am going to close this, as it does not have to do with demux"

01schau commented 1 year ago

Hi @karinlag : apology for the late reply concerning your Q: https://github.com/NorwegianVeterinaryInstitute/DemultiplexRawSequenceData/issues/66#issuecomment-1540786133

"Norway is a member state of EFSA, which is the European Food Authority in many ways. They run tests to enable laboratories in the member states to see whether their methods work correctly or not. They send out samples (or data) to the member state laboratories. We are one such lab. We then do what we do to figure out what they are testing for, and then we submit our results to them. They then let us know how we did. So, think of it as benchmarking our methods, if you will."

EFSA is the European Food Safety Authority. They do not run tests on the member states, that is up to the different EURLs to perform the ring trials. An EURL is appointed by European Commission. "It is the responsibility of the EURL-AR to provide scientific advice to the Commission on matters in relation to antimicrobial resistance". NVI is a National Reference Laboratory (NRL).