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since we're currently using the GTDB bacterial/archaeal genome database for decontamination, the automated classification approach doesn't correctly classify eukaryotes. so when cleaning eukaryotic bi…
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### Model introduction
The model is a 22B model by Mistral AI, designed for coding. It appears to be related in some way to Mixtral-8x22B, but I'm not sure exactly how it's related.
### Model URL
h…
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Decontamination process on bacterial and viral data in `KrakenProcess`. Archaeal assignments are considered contamination, as well as singular read assignments. Contamination plot in app (#10) shows s…
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When running attempting to generate report on single end data, the error
`Quitting from lines 269-291 (.snakemake.u7zo7ih9.final_report.Rmd)
Error in mutate_impl(.data, dots) :
Evaluation error:…
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This is related to issue #189 raised earlier.
My student Vladislav and I are using charcoal to decontaminate draft genome assemblies of nematodes. charcoal is wondrously efficient at ridding such …
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Hi,
I have an original matrix with shape (55000, 200). If the matrix is considered as raw matrix, how to extract a corresponding filtered matrix?
Does SoupX need two matrix (raw and filtered) to d…
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### Describe the feature request
I present this video.
https://github.com/BeeStation/BeeStation-Hornet/assets/116023863/2b65c3e7-6492-4643-abf5-540e6878605e
I thought my death was funny, but I'…
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Hi @dirkgr! Here is a feature that would be very much desirable for decontamination, but I'm not sure how difficult it would be to implement into BFF:
The essential part of the feature would be to …
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mentioned in #30
we could split classification from decontamination.
if we separated out classification from decontam, we could provide both lightweight (sourmash lca) and heavier (sourmash lca…
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### Describe the issue
I can't confirm that they did appear green in the original game's door queue dialogs, but it makes sense.
### Steps to Reproduce
1. On level 12, or any level with serious rad…