From 3f7d34ab4c7fea4db0a8495a1daa85d6d406ea70 Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Fri, 16 Aug 2024 10:34:49 +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 e6c974e..638b623 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -49,14 +49,14 @@ To address these challenges, GraphBin-Tk integrates the capabilities of GraphBin GraphBin-Tk can perform stand-alone metagenomic binning using MetaCoAG and bin refinement can be done either using GraphBin or GraphBin2. Additionally, pre-processing functionalities to run these tools and post-processing functionalities to analyse the produced results are included in GraphBin-Tk. A list of the subcommands provided in GraphBin-Tk is as follows: -| 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 | +| 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` and the paths file in `assembly_info.txt` format.