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**Project description**
A tool that identifies AMR genes, resistance-associated point mutations, and select other classes of genes using protein annotations and/or assembled nucleotide sequences.
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Hi everybody,
I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database.
I mean I have a list of predicted resistance genes from …
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I am trying to download sequence data from _E. coli_ samples within the state of Washington - it's about 1283 sequences, which I know is a lot. The problem that I am running into is that entrez_search…
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The 'https://github.com/ncbi/amr/wiki/Curated-organisms' states 'Cronobacter' in list but its usage in amr throws error- it works fine without mentioning its name in '-O' though!
amrfinder --annota…
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Hello,
I am running reference-guided genome assembly; however, I got a problem with that. It looks the problem is with the reference genome. Reference genome can be in fasta or gbk format; however, n…
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#### Current behavior:
31 genes are discovered to be uncorrelated with their corresponding reactions in `Miscellaneous`, `Isolated` and `Drug metabolism`.
| Gene| UniProtID| Reaction| GPR|…
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https://bactopia.github.io/tutorial/
I'm working through the tutorial.
```
# https://bactopia.github.io/tutorial/#build-datasets
bactopia datasets --ariba "vfdb_core,card" --species "Staphyloc…
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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**Description**
I am getting this `--tmpdir '/localscratch/mzanwar.37952706.0' is not a directory` error during BACTOPIA:CALL_VARIANTS I have attached the log and details below
```
Error execut…
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https://github.com/ncbi/amr/blob/master/README.md