From 6aa52214b013ff7c783bdda0f055900417642ac9 Mon Sep 17 00:00:00 2001
From: JeremyWesthead <jeremywesthead3@gmail.com>
Date: Thu, 27 Aug 2026 11:54:20 +0100
Subject: [PATCH] docs: add citation

---
 CITATION.bib | 11 +++++++++++
 README.md    | 21 ++++++++++++++++-----
 2 files changed, 27 insertions(+), 5 deletions(-)
 create mode 100644 CITATION.bib

diff --git a/CITATION.bib b/CITATION.bib
new file mode 100644
index 0000000..6a09b11
--- /dev/null
+++ b/CITATION.bib
@@ -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},
+}
\ No newline at end of file
diff --git a/README.md b/README.md
index 2814807..a579304 100644
--- a/README.md
+++ b/README.md
@@ -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
 ```
@@ -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)
\ No newline at end of file