add citations to readme and web app

README.md

@@ -1,12 +1,36 @@
-## ViralWasm-Consensus 
+# ViralWasm-Consensus 
 
 A client-side WebAssembly pipeline for viral consensus sequence calling. 
 
 Visit: https://niema-lab.github.io/ViralWasm-Consensus/ to run the pipeline.
 
-### ViralWasm-Consensus Offline
+## ViralWasm-Consensus Offline
 **Prerequisites**: Python (Can be downloaded here: https://www.python.org/downloads/)
 
 To run the pipeline locally without internet, download the zip file containing the offline mode of ViralWasm-Consensus: https://github.com/Niema-Lab/ViralWasm-Consensus/raw/master/viralwasm-consensus-offline.zip. After, extract the folder, and right click on the `run_website.py` file and select "Open with Python" for Windows or "Open With -> Python Launcher" for Mac. 
 
 Note: When starting the website for the first time offline, you may be prompted with a firewall warning. Click "Allow Access" to run the pipeline.
+
+## Citing ViralWasm-Consensus
+
+If you use ViralWasm-Consensus in your work, please cite:
+
+> Ji D, Aboukhalil R, Moshiri N (2023). "ViralWasm: a client-side user-friendly web application suite for viral genomics." *Bioinformatics*. btae018. [doi:10.1093/bioinformatics/btae018](https://doi.org/10.1093/bioinformatics/btae018)
+
+Please also cite the following tools used in ViralWasm-Epi:
+
+### Biowasm
+
+See https://biowasm.com/.
+
+### ViralConsensus
+
+> Moshiri N (2023). "ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data." *Bioinformatics*. btad317. [doi:10.1093/bioinformatics/btad317](https://doi.org/10.1093/bioinformatics/btad317)
+
+### Minimap2
+
+> Li H (2018). "Minimap2: pairwise alignment for nucleotide sequences." *Bioinformatics*. 34(18):3094–3100. [doi:10.1093/bioinformatics/bty191](https://doi.org/10.1093/bioinformatics/bty191)
+
+### fastp
+
+> Chen S, Zhou Y, Chen Y, Gu J (2018). "fastp: an ultra-fast all-in-one FASTQ preprocessor." *Bioinformatics*. 34(17):i884–i890. [doi:10.1093/bioinformatics/bty560](https://doi.org/10.1093/bioinformatics/bty560)

src/App.jsx

@@ -934,7 +934,12 @@ export class App extends Component {
 						{this.state.done && this.state.inputChanged && <p className="text-warning text-center">Warning: Form input has changed since last run, run again to download latest output files.</p>}
 					</div>
 				</div>
-				<footer className="d-flex w-100 justify-content-center">Source code:&nbsp;<a href="https://github.com/niema-lab/ViralWasm-Consensus/" target="_blank" rel="noreferrer">github.com/niema-lab/ViralWasm-Consensus</a>.<br /></footer>
+				<footer className="w-100 text-center px-5">
+					Source code:&nbsp;<a href="https://github.com/niema-lab/ViralWasm-Consensus/" target="_blank" rel="noreferrer">github.com/niema-lab/ViralWasm-Consensus</a>.
+					<br /><br />
+					<span>Citation: Ji D, Aboukhalil R, Moshiri N (2023). "ViralWasm: a client-side user-friendly web application suite for viral genomics." <i>Bioinformatics</i>. btae018. <a href="https://doi.org/10.1093/bioinformatics/btae018" target="_blank" rel="noreferrer">doi:10.1093/bioinformatics/btae018</a></span>
+					<br />
+				</footer>
 
 				{this.state.showOfflineInstructions &&
 					<div id="offline-instructions">