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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 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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Hello,
I'm facing a problem running the first part of vSNP pipeline.
I have Mycobacterium bovis raw reads obtained from Illumina Miniseq, with a paired end run, and I want the Mycobacterium bovis A…
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Hi, I'm actually using your programm but I found some issue such this one:
```
INFO: Starting testing: Sat May 12 20:50:59 2018
Traceback (most recent call last):
File "/pandata/me/LEPIWASP/bl…
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This gene:
fig|1205677.3.peg.1258
At PATRIC compare region view just show the originating genome and nothing else. At PubSeed I can see many other genomes. And I have seen this MANY times today!!
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Hi,
I am trying to get the taxonomy after a blast search and I came across your biopython scripts which they did look very promising.
Ihave tried them with a Mac 10.8.3 with python and biopython ins…