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I have recently tested drprg out after upgrading make_prg from https://github.com/leoisl/make_prg/releases/tag/v0.3.0 to the latest v0.4.0
The results were almost the same across ~8500 samples. How…
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Dear,
First of all, thanks for developing all tools around the AMR++ pipeline!
I have a few questions surrounding the steps after RGI main. So RGI main seems to work well, no error there. When I r…
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# Documentation
I recently needed to generate some cryptographic key material. As far as I can tell, `secrets.token_bytes()` is the recommended way of doing this, and cpython's concrete implementat…
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Hi, I'm trying to make a tree including the WH190xx sequences. https://nextstrain.org/community/babarlelephant/cov/early/china
Some are published on nmdc.
The others were assembled very naively from…
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transferred back from https://github.com/cov-lineages/pango-designation/issues/2680
In the batch uploaded today from Philippines i noticed a weird a double AA mutation in the spike in a row.
Being…
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Hi,
I'm trying to run GraffiTE in the mode that bypasses the SV calling steps but it seems to get stuck at the tsd_prep step. I was wondering if you had any idea why?
```
Loading nextflow/23.04…
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Dear,
Can some more information be given on how the three csv files for opt$marker (e.g. mutations_list_grouped_pango_codonPhased_2023-02-17_Europe.csv) , opt$smarker (mutations_special_2022-12-21.…
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I have a pool of noisy sequences with two variants that differ at indels in their ends (see figure).
`dada` with default parameters only retrieves one variant but misses the other. I think it has…
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Transferred from sars-cov-2-variants/lineage-proposals#1827
Thx @aviczhl2 .
Mutations based on JN.1: C18657T, C19716T, C21627A(S:T22N), T21738C(S:F59S) / T22928C(S:F456L), C23039G(S:Q493E), G24872…
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**System**
Bare metal
DISTRO_NAME = 'endeavouros'
DISTRO_VER = 'notfound'
VARIANT_ID = 'notfound'
SESSION_TYPE = 'x11'
DESKTOP_ENV = 'gnome'
DE_MAJ_VER = '45'
**Any…