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emo-bon / sequencing-data

The files controlling and describing the sequencing metadata
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Changes in protocols #11

Open kmexter opened 2 months ago

kmexter commented 2 months ago

A questions arising from an ARMS meeting, where we discussed that the sequencing protocols from the ARMS-MBON era and the EMO-BON era are not 100% the same

Q: Will modifications in Genoscope steps/protocols be machine-readable in downstream annotations so that meta-analyses are aware of possible comparability issues (kits, primers, cycling parameters, error correction models, sequencing chemistry, etc.), sounds like most of these steps are captured in MiXS/ASV schemas, but perhaps not all? Have they been mapped to that granularity?

In order to answer this question, and to record the necessary information, we first need to know what the genoscope protocols for wa, so, and ha are - they should be published. We can then record any differences in those protocols - not just from ARMS-MBON to EMO-BON but within EMO-BON with time.

So putting this issue on Ioulia (with a CC to Christina) for this info. Then we can discuss how to action it.

cpavloud commented 2 months ago

The library preparations and sequencing protocols were made available at the April 2024 update of the EMO BON Handbook.

kmexter commented 2 months ago

I will pass this info on to Matthias who can pass it on to the ARMS-MBON peeps