DOC: update paper

metagentools · Aug 16, 2024 · 3f7d34a · 3f7d34a
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@@ -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.