From cde5070bf2c3c1c675b7b1dedacd1f049b41a005 Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Thu, 26 Sep 2024 10:51:19 +0930 Subject: [PATCH] DOC: update paper --- paper/paper.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 022f757..4e31e27 100644 --- a/paper/paper.md +++ b/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%}