Add citation

CITATION.cff

@@ -0,0 +1,49 @@
+cff-version: 1.2.0
+message: If you use this software, please cite both the article from preferred-citation and the software itself.
+authors:
+  - family-names: Derelle
+    given-names: Romain
+  - family-names: von Wachsmann
+    given-names: Johanna
+  - family-names: Mäklin
+    given-names: Tommi
+  - family-names: Croucher
+    given-names: Nicholas J.
+  - family-names: Harris
+    given-names: Simon R.
+  - family-names: Lees
+    given-names: John A.
+title: Split K-mer Analysis (version 2)
+version: 0.3.11
+url: https://github.com/bacpop/ska.rust
+date-released: '2024-09-25'
+preferred-citation:
+  authors:
+    - family-names: Derelle
+      given-names: Romain
+    - family-names: von Wachsmann
+      given-names: Johanna
+    - family-names: Mäklin
+      given-names: Tommi
+    - family-names: Hellewell
+      given-names: Joel
+    - family-names: Russell
+      given-names: Timothy
+    - family-names: Lalvani
+      given-names: Ajit
+    - family-names: Chindelevitch
+      given-names: Leonid
+    - family-names: Croucher
+      given-names: Nicholas J.
+    - family-names: Harris
+      given-names: Simon R.
+    - family-names: Lees
+      given-names: John A.
+  title: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
+  doi: 10.1101/gr.279449.124
+  url: http://genome.cshlp.org/content/34/10/1661.abstract
+  type: article-journal
+  pages: 1661-1673
+  year: '2024'
+  conference: {}
+  publisher: {}

README.md

@@ -28,9 +28,9 @@ SKA can only align SNPs further than the k-mer length apart, and does not use a
 
 ### Citation
 
-Romain Derelle, Johanna von Wachsmann, Tommi Mäklin, Joel Hellewell, Timothy Russell, Ajit Lalvani, Leonid Chindelevitch, Nicholas J. Croucher, Simon R. Harris, John A. Lees (2024).
-**Seamless, rapid and accurate analyses of outbreak genomic data using Split _k_-mer Analysis**
-*Genome Research*
+Romain Derelle, Johanna von Wachsmann, Tommi Mäklin, Joel Hellewell, Timothy Russell, Ajit Lalvani, Leonid Chindelevitch, Nicholas J. Croucher, Simon R. Harris, John A. Lees (2024). Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis. Genome Research, 34(10), 1661–1673.
+
+https://genome.cshlp.org/content/34/10/1661.abstract
 
 ## Documentation
 

src/lib.rs

@@ -1,4 +1,4 @@
-//! Split k-mer analysis (version 2)  uses exact matching of split k-mer sequences to align closely related
+//! Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related
 //! sequences, typically small haploid genomes such as bacteria and viruses.
 //!
 //! SKA can only align SNPs further than the k-mer length apart,
@@ -37,6 +37,10 @@
 //! - [From genomes to trees](https://www.bacpop.org/guides/building_trees_with_ska/).
 //! - [Filtering options](https://www.bacpop.org/guides/snp_alignment_with_ska/).
 //!
+//! Papers:
+//! - [Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis ](https://genome.cshlp.org/content/34/10/1661.abstract).
+//! - [skalo: using SKA split k-mers with coloured de Brujin graphs to genotype indels](https://www.biorxiv.org/content/10.1101/2024.10.02.616334v1).
+//!
 //! Command line usage follows. For API documentation and usage, see the [end of this section](#api-usage).
 //!
 //! # Usage