Add package: 2025_Lazaridis_Yamnaya

[Kavlahkaff]

Linked to #65

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[Kavlahkaff]

@delphis-bot create recipe

[Kavlahkaff]

Hi @TCLamnidis, could you have a look at this? Just to double check I made the correct entries for udg and library. I have startet with the janno but will need some time for it since its quite large.

[TCLamnidis]

Hi @Kavlahkaff
After having a look, I don't think the UDG/Strandedness info is quite correct. If you look at column AK of OnlineTable1(inds.new.data) in the Supplementary Tables file, you can see the attributes for the different libraries merged for each individual. They are encoded as follows:

minus=no.damage.correction,
half=damage.retained.at.last.position,
plus=damage.fully.corrected,
ds=double.stranded.library.preparation,
ss=single.stranded.library.preparation

While you have correctly marked mixes of ds/ssDNA libraries as ds, any IDs that only contain ss.* entries should be marked as ss in the SSF.
Also, the UDG column should only be minus in cases where at least one of the libraries has received NO UDG-treament (i.e. minus). When combining multiple libraries, the column should contain the value of the least treated library. (So half if no minus libraries and at least 1 half library got combined.)

Also, note that ss.USER in this case would be equivalent to ss.half, since in the paper they state:

We treated DNA extracts with USER (NEB) during library preparation to cut DNA at uracils; this treatment is inefficient at terminal uracils and leaves a damage pattern expected for ancient DNA at the terminal bases that can be filtered out for downstream analysis while allowing a library to be authenticated as old.

[Kavlahkaff]

@delphis-bot create recipe

[Kavlahkaff]

@delphis-bot create recipe

[Kavlahkaff]

@TCLamnidis this is ready for review now.

[TCLamnidis]

I have moved the provided janno to here: https://github.com/poseidon-framework/minotaur-archive/blob/2025_Lazaridis_Yamnaya/2025_Lazaridis_Yamnaya/2025_Lazaridis_Yamnaya.janno_provided

I will delete it from the recipe itself.

(btw, the janno seems to have some formatting issues. Will need some manual curation before coalescing).

[TCLamnidis]

@delphis-bot create recipe