DOC: update paper

paper/paper.md

@@ -71,9 +71,9 @@ The following inputs are required to run the `metacoag` subcommand.
 
 * Contigs file
 * Assembly graph file(s)
-* A delimited file containing the contig identifier and its average read coverage for each contig - this can be obtained by running a read coverage calculation tool such as CoverM [https://github.com/wwood/CoverM](https://github.com/wwood/CoverM) or Koverage [@Roach:2024]
+* A delimited file containing the contig identifier and its average read coverage for each contig - can be obtained by running a read coverage calculation tool such as CoverM ([https://github.com/wwood/CoverM](https://github.com/wwood/CoverM)) or Koverage [@Roach:2024]
 
-The assembly graph files can vary depending on the assembler used to generate the contigs. The metaSPAdes version requires the assembly graph file in `.gfa` format and the paths file in `.paths` format. The MEGAHIT version requires the assembly graph file in `.gfa` format. The metaFlye version requires the assembly graph file `assembly_graph.gfa` and the paths file `assembly_info.txt` from the final assembly output.
+The assembly graph files can vary depending on the assembler used to generate the contigs. The metaSPAdes version requires the assembly graph file in `.gfa` format and the paths file corresponding to the contigs file in `.paths` format. The MEGAHIT version requires the assembly graph file in `.gfa` format. The metaFlye version requires the assembly graph file `assembly_graph.gfa` and the paths file `assembly_info.txt` from the final assembly output.
 
 ### Outputs
 
@@ -87,7 +87,7 @@ The following outputs will be generated by the `metacoag` subcommand.
 
 ### Tool/processing function
 
-If a delimited text file is not available, the initial binning result can be formatted using the `prepare` subcommand into a delimited text file  that represents each contig and its bin identifier. This function allows users to format binning results from any existing metagenomic binning tool.
+If a delimited text file is not available, the initial binning result can be formatted using the `prepare` subcommand into a delimited text file  that represents each contig and its bin identifier. This function allows users to format binning results from any metagenomic binning tool.
 
 ### Inputs
 
@@ -108,7 +108,7 @@ A formatted initial binning result from the `prepare` subcommand can be improved
 The following inputs are required to run the `graphbin` subcommand.
 
 * Contigs file
-* Assembly graph file(s) - can vary depending on the assembler used to generate the contigs (refer to inputs under `metacoag`)
+* Assembly graph file(s) - can vary depending on the assembler used (refer to inputs under `metacoag`)
 * A delimited text file containing the initial binning result
 
 ### Outputs
@@ -129,9 +129,9 @@ A formatted initial binning result from the `prepare` subcommand can be improved
 The following inputs are required to run the `graphbin2` subcommand.
 
 * Contigs file
-* Assembly graph file(s) - can vary depending on the assembler used to generate the contigs (refer to inputs under `metacoag`)
+* Assembly graph file(s) - can vary depending on the assembler used (refer to inputs under `metacoag`)
 * A delimited text file containing the initial binning result
-* A delimited file containing the contig identifier and its average read coverage for each contig
+* A delimited file containing the contig identifier and its average read coverage for each contig - can be obtained by running a read coverage calculation tool (refer to inputs under `metacoag`)
 
 ### Outputs
 
@@ -190,7 +190,7 @@ The following inputs are required to run the `evaluate` subcommand.
 
 ### Outputs
 
-A text file containing the $K \times S$ matrix and the calculated evaluation metrics will be generated by the `evaluate` subcommand. These metrics can be plotted for comparison between the initial binning result and the refined binning result as shown in \autoref{fig3}.
+A text file containing the $K \times S$ matrix and the calculated evaluation metrics will be generated by the `evaluate` subcommand. These metrics can be plotted for comparison between the initial binning result and the refined binning result using custom code as shown in \autoref{fig3}.
 
 ![Comparison of evaluation metrics for the intiial binning result from MetaCoAG and the refined binning result from GraphBin for the Sim-5G+metaSPAdes dataset.\label{fig3}](gbintk_metrics_comparison.svg){width=70%}