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DOC: update paper
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Vini2 committed Aug 16, 2024
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Expand Up @@ -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}).
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