Update README.md

README.md

@@ -6,12 +6,31 @@
 
 Reads directly extracted from the reference genome are simulated without any mutations/variants. If you want to have variants in your simulated data, you can first apply a set of variants to the reference using [bcftools](http://www.htslib.org/download/) and use that as the input to the *squigulator*.
 
+Preprint: https://www.biorxiv.org/content/10.1101/2023.05.09.539953v1<br/>
+SLOW5 ecosystem: https://hasindu2008.github.io/slow5<br/>
+
 ![squigulator](docs/img/example.svg)
 
 [![GitHub Downloads](https://img.shields.io/github/downloads/hasindu2008/squigulator/total?logo=GitHub)](https://github.com/hasindu2008/squigulator/releases)
 [![BioConda Install](https://img.shields.io/conda/dn/bioconda/squigulator?label=BioConda)](https://anaconda.org/bioconda/squigulator)
 [![x86_64](https://github.com/hasindu2008/squigulator/actions/workflows/c-cpp.yml/badge.svg)](https://github.com/hasindu2008/squigulator/actions/workflows/c-cpp.yml)
 
+
+Please cite the following in your publications when using *squigulator*:
+
+> Gamaarachchi, H., Ferguson, J. M., Samarakoon, H., Liyanage, K., & Deveson, I. W. (2023). Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters. bioRxiv, 2023-05.
+
+```
+@article{gamaarachchi2023squigulator,
+  title={Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters},
+  author={Gamaarachchi, Hasindu and Ferguson, James M and Samarakoon, Hiruna and Liyanage, Kisaru and Deveson, Ira W},
+  journal={bioRxiv},
+  pages={2023--05},
+  year={2023},
+  publisher={Cold Spring Harbor Laboratory}
+}
+```
+
 ## Background story
 
 *squigulator* started as *ssssim* (Stupidly Simple Signal Simulator). For an experiment, [kisarur](https://github.com/kisarur) wanted some simulated data. After [hiruna72](https://github.com/hiruna72) trying ~3 days to get an existing simulator installed (dependency and compatibility issues), I thought that writing a simple tool from scratch is easier. Indeed, that is when writing BLOW5 files. Writing over complicated formats like FAST5 or POD5 would consume months and I would not think about writing a simulator in the first place then.