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11 changes: 11 additions & 0 deletions CITATION.bib
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
@article{Westhead2025,
title = {Characterizing the Performance of an Antibiotic Resistance Prediction Tool, Gnomonicus, Using a Diverse Test Set of 2,663 {{Mycobacterium}} Tuberculosis Samples},
author = {Westhead, Jeremy and Baker, Catriona S. and Brouard, Marc and Colpus, Matthew and Constantinides, Bede and Hall, Alexandra and Knaggs, Jeff and Alves, Marcela Lopes and Spies, Ruan and Thai, Hieu and Surrall, Sarah and Govender, Kumeren and Peto, Timothy E.A. and Crook, Derrick W. and Omar, Shaheed V. and Turner, Robert and Fowler, Philip W.},
year = 2025,
journal = {Microbial Genomics},
volume = {11},
number = {12},
pages = {001592},
publisher = {Microbiology Society,},
doi = {10.1099/mgen.0.001592},
}
21 changes: 16 additions & 5 deletions README.md
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Expand Up @@ -5,17 +5,18 @@ Re-implementation of [gumpy](https://github.com/oxfordmmm/gumpy) in Rust for spe

## Installation

### Rust crate
### CLI
```
cargo add grumpy
cargo install grumpy
```

### CLI
### As a dependency for development
#### Rust crate
```
cargo install grumpy
cargo add grumpy
```

### Python package
#### Python package
```
pip install bio-grumpy
```
Expand All @@ -35,3 +36,13 @@ cargo install cargo-tarpaulin
# Generate an HTML coverage report
cargo tarpaulin --no-dead-code --engine llvm --out html
```

## Citation
If you use `grumpy` in your work, please cite:
```
Westhead J, Baker CS, Brouard M, Colpus M, Constantinides B, Hall A, Knaggs J, Lopes Alves M, Spies R, Thai H, Surrall S, Govender K, Peto TEA, Crook DW, Omar SV, Turner R, Fowler PW
Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 Mycobacterium tuberculosis samples
Microbial Genomics 11:001592 doi:10.1099/mgen.0.001592
```

A BibTeX citation is included [here](CITATION.bib)
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