DOC: update paper

paper/paper.md

@@ -72,7 +72,7 @@ GraphBin-Tk can perform stand-alone metagenomic binning using MetaCoAG and bin r
 
 ## Binning, preparing binning results and bin refinement
 
-GraphBin-Tk supports metagenome assemblies generated from three popular metagenome assemblers; metaSPAdes [@Nurk:2017] and MEGAHIT [@Li:2015] for short-read sequencing data and metaFlye [@Kolmogorov:2020] for long-read sequencing data. GraphBin-Tk can be launched using the command `gbintk`. A user can start the analysis by running the `metacoag` subcommand to bin a metagenomic dataset and obtain MAGs as shown in \autoref{fig1}. The inputs required are the contigs file, the assembly graph files and the read coverage of contigs. The read coverage of contigs can be obtained by running a coverage calculation tool such as Koverage [@Roach:2024]. The MetaCoAG binning result can be formatted using the `prepare` subcommand into a delimited text file such as `.csv` of `.tsv` that represents each contig and its bin name. This formatted binning result can be improved by providing to either GraphBin or GraphBin2 using the subcommands `graphbin` or `graphbin2` along with the contigs file, the assembly graph files and the read coverage of contigs (refer to \autoref{fig1}). 
+GraphBin-Tk supports metagenome assemblies generated from three popular metagenome assemblers; metaSPAdes [@Nurk:2017] and MEGAHIT [@Li:2015] for short-read sequencing data and metaFlye [@Kolmogorov:2020] for long-read sequencing data. GraphBin-Tk can be launched using the command `gbintk`. A user can start the analysis by running the `metacoag` subcommand to bin a metagenomic dataset and obtain MAGs as shown in \autoref{fig1}. The inputs required are the contigs file, the assembly graph files and the read coverage of contigs. The read coverage of contigs can be obtained by running a coverage calculation tool such as Koverage [@Roach:2024]. The MetaCoAG binning result can be formatted using the `prepare` subcommand into a delimited text file such as `.csv` or `.tsv` that represents each contig and its bin name. This formatted binning result can be improved by providing to either GraphBin or GraphBin2 using the subcommands `graphbin` or `graphbin2` with the contigs file, the assembly graph files and the read coverage of contigs (\autoref{fig1}). 
 
 ## Visualisation