-
```
Running: amrfinder -n AF01.ffn -d amrfinderdb/ -o antimicrobial-resistance/AF01-gene-report.txt --ident_min -1 --coverage_min 0.5 --translation_table 11 --threads 4
Software directory: '/bac…
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ID | Label | Comment
-- | -- | --
APOLLO_SV:00000570 | Employment status | in PR under 'employment information'
ARO:3004306 | Methicillin resistant Staphylococcus aureus | in PR under 'antimicrobia…
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Sometimes in workflows (Nextflow, Cromwell, etc...) I find it it's nicer to just include multiple packages in a single container to avoid have numerous steps and the pulling/starting/stopping of conta…
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currently the AMR folder is named `antimicrobial_resistance` change it to `antimicrobial-resistance` to match others (e.g. `quality-control`
This will change things so will have to wait for v1.6.0
-
Hi,
I am trying to install Bactopia and test it with few Salmonella genomes. However, after creating the conda environment and downloading the necessary databases
```
conda create -y -n bactopia …
-
https://bactopia.github.io/quick-start/
```
conda create -y -n bactopia -c conda-forge -c bioconda bactopia
conda activate bactopia
bactopia datasets
```
created the following folders instead of…
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Propose adding the term "mediates resistance to antibiotics" to the ontology, as a single term that cross references the CARD ontology as well as GO term 'GO:0046677 - response to antibiotic'. As Ama…
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hi sir:
It is a good job in ,
i want to get the AST ,and use your methd to predict many Pseudomonas aeruginosa resistance,
thanks
-
Hi,
I am trying to use bactopia with 2 samples (i have qc-ed llumina and nanopore fastq so I am using the hybrid assembly option here) but keeps exiting with an error during the assembly step. The …
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**Description**
Fresh install of bactopia & build of datasets, testing on a single sample. Fails on minmer_query with unrecognized arguments to sourmash.
```
$ bactopia --sample 20191007_31_pBA…