From d224ecb3783f76a4d652dc8d1302c89d21bb8f3c Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Fri, 16 Aug 2024 10:27:12 +0930 Subject: [PATCH] DOC: update paper --- paper/paper.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index c7d4406..f1f6e92 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -51,14 +51,14 @@ GraphBin-Tk can perform stand-alone metagenomic binning using MetaCoAG and bin r | Subcommand | Tool/processing functionality | Inputs required | |-------------|------------------------------------------------------------|-------------------------------------------------------------------------------------------------| -| `graphbin` | Bin refinement tool GraphBin | Contigs, assembly graph file(s)[^1], initial binning result | -| `graphbin2` | Bin refinement tool GraphBin2 | Contigs, assembly graph file(s), initial binning result, coverage of contigs | -| `metacoag` | Binning tool MetaCoAG | Contigs, assembly graph file(s), coverage of contigs | -| `prepare` | Format initial binning results for GraphBin and GraphBin2 | Folder containing the initial binning result | -| `visualise` | Visualise initial and refined binning results on the assembly graph | Assembly graph file(s), initial binning result, final binning result | -| `evaluate` | Evaluate binning results given a ground truth | Binning result, ground truth | - -[^1]: The assembly graph files can vary depending on the assembler used to generate the contigs. metaSPAdes version requires the assembly graph file `.gfa` format and the paths file `contigs.paths`. MEGAHIT version requires the assembly graph file in `.gfa`. metaFlye version requires the assembly graph file `assembly_graph.gfa` format and the paths file in `assembly_info.txt` format. +| graphbin | Bin refinement tool GraphBin | Contigs, assembly graph file(s)[^1], initial binning result | +| graphbin2 | Bin refinement tool GraphBin2 | Contigs, assembly graph file(s), initial binning result, coverage of contigs | +| metacoag | Binning tool MetaCoAG | Contigs, assembly graph file(s), coverage of contigs | +| prepare | Format initial binning results for GraphBin and GraphBin2 | Folder containing the initial binning result | +| visualise | Visualise initial and refined binning results on the assembly graph | Assembly graph file(s), initial binning result, final binning result | +| evaluate | Evaluate binning results given a ground truth | Binning result, ground truth | + +[^1]: The assembly graph files can vary depending on the assembler used to generate the contigs. metaSPAdes version requires the assembly graph file `.gfa` format and the paths file `contigs.paths`. MEGAHIT version requires the assembly graph file in `.gfa`. metaFlye version requires the assembly graph file `assembly_graph.gfa` and the paths file in `assembly_info.txt` format. 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 `.csv` file that represents each contig and its bin name. This formatted binning result can be provided 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}).