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Sample ```Mycobacterium_bovis_BCG_Danish_1331_r250_e0_m0_24070812``` is being flagged as MTB because Afanc identifies this sample as Bovis, however, the top hit is named ```Mycobacterium tuberculosis …
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Hello,
I'm currently working on Mycobacterium caprae and Mycobacterium bovis. These subspecies of the M. tuberculosis complex are phylogenetically very similar, so the task of identifying them is n…
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Hi,
some of the terms are not available in the template and hence would like to request for their addition.
Bacteria species
Escherichia coli K-12 W3110 Tax. ID: 316407
Klebsiella pneumoniae A…
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If I take a look at the current Galaxy cgMLST options, I can see an option for **Mycobacterium tuberculosis/bovis/africanum/canettii** and **Klebsiella pneumoniae/variicola/quasipneumoniae** (https://…
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I download MLST database by `download_mlst_databases` and make `export MLST_DATABASES=/export/data/user/MLSTdb`
```
(base) [user@bigmem01 STRP-2020]$ get_sequence_type -a
Achromobacter spp
Acineto…
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Hi Tod,
I've been trying the nanopore support of vSNP3 and I think it still needs to be optimized.
First, when installing vSNP3 with conda, it lacks 2 dependencies: vcftools and bcftools. To ge…
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Hello!
I have downloaded vsnp3 on my MacOS (M2 Chip) using conda and I am currently trying to [Run test with AF2122 (Mycobacterium bovis)](https://github.com/USDA-VS/vSNP3/tree/main?tab=readme-ov-…
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Do you happen to have taxon identifiers for the training data in this file?
https://genome.cshlp.org/content/suppl/2018/03/22/gr.228429.117.DC1/Supplemental_Table_S1.xlsx
It's currently difficu…
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