DOC: add pages for read the docs

metagentools · Aug 15, 2024 · 1b738ca · 1b738ca
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diff --git a/docs/evaluate.md b/docs/evaluate.md
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+# Evaluating binning results
diff --git a/docs/graphbin2_intro.md b/docs/graphbin2_intro.md
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+# GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
diff --git a/docs/graphbin2_preprocess.md b/docs/graphbin2_preprocess.md
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+# Preprocessing for GraphBin2
diff --git a/docs/graphbin2_usage.md b/docs/graphbin2_usage.md
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+# Using GraphBin2
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+# GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
diff --git a/docs/graphbin_preprocess.md b/docs/graphbin_preprocess.md
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+# Preprocessing for GraphBin
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+# Using GraphBin
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 # GraphBin-Tk: assembly graph-based metagenomic binning toolkit
 
-GraphBin-Tk combines assembly graph-based metagenomic bin-refinement and binning techniques [GraphBin](https://github.com/metagentools/GraphBin), [GraphBin2](https://github.com/metagentools/GraphBin2) and [MetaCoAG](https://github.com/metagentools/MetaCoAG) along with support functionality to visualise and evaluate results, into one comprehensive toolkit.
+GraphBin-Tk combines assembly graph-based metagenomic bin-refinement and binning techniques [GraphBin](https://github.com/metagentools/GraphBin), [GraphBin2](https://github.com/metagentools/GraphBin2) and [MetaCoAG](https://github.com/metagentools/MetaCoAG) along with support functionality to visualise and evaluate results, into one comprehensive toolkit.
+
+![](images/gbintk_workflow.png)
+
+## Available commands
+
+Run `gbintk --help` or `gbintk -h` to list the help message for GraphBin-Tk.
+
+```shell
+Usage: gbintk [OPTIONS] COMMAND [ARGS]...
+
+  gbintk (GraphBin-Tk): Assembly graph-based metagenomic binning toolkit
+
+Options:
+  -v, --version  Show the version and exit.
+  -h, --help     Show this message and exit.
+
+Commands:
+  graphbin   GraphBin: Refined Binning of Metagenomic Contigs using...
+  graphbin2  GraphBin2: Refined and Overlapped Binning of Metagenomic...
+  metacoag   MetaCoAG: Binning Metagenomic Contigs via Composition,...
+  prepare    Format the initial binning result from an existing binning tool
+  visualise  Visualise binning and refinement results
+  evaluate   Evaluate the binning results given a ground truth
diff --git a/docs/install.md b/docs/install.md
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+# Installing GraphBin-Tk
diff --git a/docs/metacoag_intro.md b/docs/metacoag_intro.md
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+# MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
diff --git a/docs/metacoag_preprocess.md b/docs/metacoag_preprocess.md
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+# Preprocessing for MetaCoAG
diff --git a/docs/metacoag_usage.md b/docs/metacoag_usage.md
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+# Using MetaCoAG
diff --git a/docs/prepare.md b/docs/prepare.md
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+# Formatting binning results for GraphBin/GraphBin2
diff --git a/docs/visualise.md b/docs/visualise.md
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+# Visualising binning results
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		# GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
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		# GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
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		# MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
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		# Formatting binning results for GraphBin/GraphBin2