GIT: Merge branch 'main' into JOSS

metagentools · Sep 24, 2024 · cd6414f · cd6414f
2 parents 6da3a4f + c64b631
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diff --git a/docs/graphbin2_usage.md b/docs/graphbin2_usage.md
@@ -26,9 +26,8 @@ Options:
                                   [default: 5]
   --threshold FLOAT               threshold for determining inconsistent
                                   vertices.  [default: 1.5]
-  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
-                                  a comma (,), a semicolon (;), a tab ($'\t'),
-                                  a space (" ") and a pipe (|)  [default: ,]
+  --delimiter [comma|tab]         delimiter for input/output results. Supports
+                                  a comma and a tab.  [default: comma]
   --nthreads INTEGER              number of threads to use.  [default: 8]
   -h, --help                      Show this message and exit.
 ```

diff --git a/docs/graphbin_usage.md b/docs/graphbin_usage.md
@@ -24,9 +24,8 @@ Options:
                                   propagation algorithm  [default: 100]
   --diff_threshold FLOAT RANGE    difference threshold for label propagation
                                   algorithm  [default: 0.1; 0<=x<=1]
-  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
-                                  a comma (,), a semicolon (;), a tab ($'\t'),
-                                  a space (" ") and a pipe (|)  [default: ,]
+  --delimiter [comma|tab]         delimiter for input/output results. Supports
+                                  a comma and a tab.  [default: comma]
   -h, --help                      Show this message and exit.
 ```
 

diff --git a/docs/index.md b/docs/index.md
@@ -4,22 +4,17 @@ GraphBin-Tk combines assembly graph-based metagenomic bin-refinement and binning
 
 ![](images/gbintk_workflow.png)
 
-Run `gbintk --help` or `gbintk -h` to list the help message for GraphBin-Tk.
+If you use GraphBin-Tk in your work, please cite the relevant tools.
 
-```shell
-Usage: gbintk [OPTIONS] COMMAND [ARGS]...
+**GraphBin**
+> Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin. GraphBin: Refined binning of metagenomic contigs using assembly graphs. Bioinformatics, Volume 36, Issue 11, June 2020, Pages 3307–3313, DOI: [https://doi.org/10.1093/bioinformatics/btaa180](https://doi.org/10.1093/bioinformatics/btaa180)
 
-  gbintk (GraphBin-Tk): Assembly graph-based metagenomic binning toolkit
+**GraphBin2**
+> Vijini G. Mallawaarachchi, Anuradha S. Wickramarachchi, and Yu Lin. GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 8:1-8:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020). DOI: [https://doi.org/10.4230/LIPIcs.WABI.2020.8](https://doi.org/10.4230/LIPIcs.WABI.2020.8)
 
-Options:
-  -v, --version  Show the version and exit.
-  -h, --help     Show this message and exit.
+> Mallawaarachchi, V.G., Wickramarachchi, A.S. & Lin, Y. Improving metagenomic binning results with overlapped bins using assembly graphs. Algorithms Mol Biol 16, 3 (2021). DOI:  [https://doi.org/10.1186/s13015-021-00185-6](https://doi.org/10.1186/s13015-021-00185-6)
 
-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
-```
+**MetaCoAG**
+> Mallawaarachchi, V., Lin, Y. (2022). MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs. In: Pe'er, I. (eds) Research in Computational Molecular Biology. RECOMB 2022. Lecture Notes in Computer Science(), vol 13278. Springer, Cham. DOI: [https://doi.org/10.1007/978-3-031-04749-7_5](https://doi.org/10.1007/978-3-031-04749-7_5)
+
+> Vijini Mallawaarachchi and Yu Lin. Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. Journal of Computational Biology 2022 29:12, 1357-1376. DOI: [https://doi.org/10.1089/cmb.2022.0262](https://doi.org/10.1089/cmb.2022.0262)
diff --git a/docs/metacoag_usage.md b/docs/metacoag_usage.md
@@ -42,9 +42,8 @@ Options:
                                   0<=x<=1]
   --min_bin_size INTEGER          minimum size of a bin to output in base
                                   pairs (bp).  [default: 200000]
-  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
-                                  a comma (,), a semicolon (;), a tab ($'\t'),
-                                  a space (" ") and a pipe (|)  [default: ,]
+  --delimiter [comma|tab]         delimiter for input/output results. Supports
+                                  a comma and a tab.  [default: comma]
   --nthreads INTEGER              number of threads to use.  [default: 8]
   -h, --help                      Show this message and exit.
 ```