STATE OF FIELD: No comparison to AMR detection tools with summary utilities

[fmaguire]

Current antimicrobial resistance gene finding tools can detect the genes from either genome assemblies or sequencing reads but do not exclusively report a genetic profile for the presence of CP genes across all the genome assemblies and neither provide the ability to extract and visualize the co-carriage of multiple CP genes. Therefore, to address this need, we describe here a lightweight R package, CPgeneProfiler that scans bacterial genome sequences to detect the presence of CP genes using R framework

While there are no existing tools that produce these summaries for only CP genes, there are several packages/tools that allow either generation of comparative tables across genomes and some visualisations for a much more comprehensive AMR gene complement e.g.
sraX allows generation of numerous navigable resistome comparison visualisations,
RGI has a heatmap feature that allows users to produce similar comparison visualisations across multiple genomes,
and abricate has a command to generate a summary table from multiple genomes.

These need mentioned for point of comparison and the benefits of the specialisation of CPGeneProfiler carefully articulated.

[ramadatta]

We agree with reviewer on comparison to AMR detection tools with summary utilities. In regard to that, we have rephrased in the manuscript how other AMR detection tools are undeniably useful in generating summary tables and visualizations with full AMR complement. And also, we have mentioned on the benefits of the specialization of CPgeneProfiler tool.