Update paper.md

paper.md

@@ -58,7 +58,7 @@ To this end, several freely available bioinformatics tools such as ``ABRicate``
 
 # Statement of Need 
 
-Undeniably, all the above-mentioned tools are focused around the antimicrobial-resistant genes and tools such as ABRicate and CARD-RGI can even generate comparative tables across genomes and sraX can help in visualization of comprehensive AMR gene complement. Nevertheless, they do not readily generate a genetic profile for the presence of CP genes, extract and visualize the cocarriage of CP genes. Achieving this currently necessitates a restructuring and transformation of the output from these tools. Furthermore, in the research settings where it is crucial to quickly examine the transmission of CP genes, it is useful to have a tool that is catered to CP gene dataset that provides easily interpretable visualizations and statistics. Therefore, to address this need, we describe here a lightweight R package, **CPgeneProfiler** that scans multiple bacterial genome assemblies to detect and visualize the presence of CP genes and their cocarriage using the R framework. Additionally, this package also allows to assess the size of CP contigs to check if the CP genes are distributed on the particular sequence size by generating the contig length distribution plots. 
+Undeniably, all the above-mentioned tools are focused around the antimicrobial-resistant genes and tools such as ABRicate and CARD-RGI can even generate comparative tables across genomes and sraX can help in visualization of comprehensive AMR gene complement. Nevertheless, they do not readily generate a genetic profile for the presence of CP genes, extract and visualize the set intersections of cocarriage of CP genes. Achieving this currently necessitates a restructuring and transformation of the output from these tools. Furthermore, in the research settings where it is crucial to quickly examine the transmission of CP genes, it is useful to have a tool that is catered to CP gene dataset that provides easily interpretable visualizations and statistics. Therefore, to address this need, we describe here a lightweight R package, **CPgeneProfiler** that scans multiple bacterial genome assemblies to detect and visualize the presence of CP genes and their cocarriage using the R framework. Additionally, this package also allows to assess the size of CP contigs to check if the CP genes are distributed on the particular sequence size by generating the contig length distribution plots. 
 
 # Implementation