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First version of quality control pathogens page #240

Merged
merged 16 commits into from
Nov 28, 2023
Merged

First version of quality control pathogens page #240

merged 16 commits into from
Nov 28, 2023

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EvaGarciaAlvarez
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@EvaGarciaAlvarez EvaGarciaAlvarez requested a review from a team as a code owner October 10, 2023 09:45
@bedroesb bedroesb linked an issue Nov 6, 2023 that may be closed by this pull request
Quality control - Pathogen characterisation - Wastewater use case #97
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@lauportell
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I think the page is nice and clear!
I don't have many comments. Maybe only for consistency, in NGS pathogens data and NGS analysis sections, it mentions "Considerations for sequencing data" and "Considerations for analysing sequencing data". Do we want to leave only "Considerations" to be aligned with the other secions and pages? I am okay with both approaches, it won't change much :)

bedroesb
bedroesb reviewed Nov 24, 2023
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pathogen-characterisation/quality-control.md Outdated
* Quality control of the quantitative analytical detection
* Standard calibrated reference material (such as EURM-019 / EURM-014 single stranded RNA provided by the Joint Research Center)

In particular the European Commission Recommendation (EU) 2021/472 of 17 March 2021 has advocated the use of a common approach to establish a systematic surveillance of SARS-CoV-2 and its variants in wastewaters in the EU (OJ L 98 19.03.2021, p. 3, CELEX: Specific Quality Standards are indicated in this Recommendation document: standards for PCR/Digital-PCR (polymerase chain reaction), shortly described below:
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EU (OJ L 98 19.03.2021, p. 3, CELEX: Specific Quality Standards are indicated in this Recommendation document: standards for PCR/Digital-PCR (polymerase chain reaction), shortly described below:

This sentence is missing a parenthesis and is difficult to read.

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Indeed, thanks! I've modified it

bedroesb
bedroesb reviewed Nov 24, 2023
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pathogen-characterisation/quality-control.md Outdated

Further information on wastewater quality control can be found in Wastewater QC workflow in GalaxyTrakr (SSQuAWK3) (protocols.io) protocol that has a nice listing of quality indicators that were defined in the context of SARS-CoV-2, but are easily generalizable.
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"protocols.io" seems to miss a link?

@EvaGarciaAlvarez EvaGarciaAlvarez merged commit c6e5517 into elixir-europe:main Nov 28, 2023
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@lauportell lauportell lauportell approved these changes

@bedroesb bedroesb bedroesb approved these changes

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Quality control - Pathogen characterisation - Wastewater use case
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@EvaGarciaAlvarez @lauportell @bedroesb