update citations

fixes #125

README.md

@@ -8,10 +8,14 @@ Clockwork takes fastq input and outputs standard VCF files as output
 
 Please see the [clockwork wiki page](https://github.com/iqbal-lab-org/clockwork/wiki) for documentation.
 
-**Citation**
-If you use Clockwork please cite the following paper,  whete it was introduced and benchmarked 
+## Citation
+If you use Clockwork for variant calling please cite the following paper, where it was introduced and benchmarked:  
 
-"Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes"
-Hunt et al. Genome Biol
-. 2022 Jul 5;23(1):147.
-doi: 10.1186/s13059-022-02714-x.
+"Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes". Hunt et al. Genome Biol. 2022 Jul 5;23(1):147.
+[doi: 10.1186/s13059-022-02714-x.](https://doi.org/10.1186/s13059-022-02714-x)
+
+Whilst Minos is the novel part of the Clockwork variant calling pipeline, it uses several other tools. Please also cite:
+* Minimap2 https://doi.org/10.1093/bioinformatics/bty191
+* SAMtools https://doi.org/10.1093/gigascience/giab008
+* Cortex https://doi.org/10.1038/ng.1028
+* Trimmomatic: https://doi.org/10.1093/bioinformatics/btu170