GIT: Merge branch 'main' into JOSS

metagentools · Sep 20, 2024 · 49778d3 · 49778d3
2 parents 7c1c2b1 + 6cb522e
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diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 [![Documentation Status](https://readthedocs.org/projects/gbintk/badge/?version=latest)](https://gbintk.readthedocs.io/en/latest/?badge=latest)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-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 additional processing functionality to visualise and evaluate results, into one comprehensive toolkit.
 
 <p align="center">
   <img src="https://raw.githubusercontent.com/metagentools/gbintk/master/docs/images/gbintk_workflow.png" width="800" title="Initial binning" alt="Initial binning">

diff --git a/docs/evaluate.md b/docs/evaluate.md
@@ -23,7 +23,7 @@ Options:
 
 ### Input Format
 
-`visualise` subcommand takes in 2 files as inputs.
+`evaluate` subcommand takes in 2 files as inputs.
 
 * Binning result containing the comma separated records of `contig id,bin number` (in `.csv` format)
 * Ground truth annotations containing the comma separated records of `contig id, groud truth bin` (in `.csv` format)

diff --git a/docs/graphbin2_preprocess.md b/docs/graphbin2_preprocess.md
@@ -20,7 +20,7 @@ gbintk prepare --assembler megahit ----resfolder /path/to/folder_with_binning_re
 # For Flye
 gbintk prepare --assembler flye ----resfolder /path/to/folder_with_binning_result --output /path/to/output_folder
 ```
-More details on the `prepare` subcommand can be found in the [Support](https://gbintk.readthedocs.io/en/latest/prepare/) section of this documentation.
+More details on the `prepare` subcommand can be found in the [Processing](https://gbintk.readthedocs.io/en/latest/prepare/) section of this documentation.
 
 Formatted binning result will be stored in a file named `initial_contig_bins.csv` in the output folder provided.
 

diff --git a/docs/index.md b/docs/index.md
@@ -1,6 +1,6 @@
 # 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 additional processing functionality to visualise and evaluate results, into one comprehensive toolkit.
 
 ![](images/gbintk_workflow.png)
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -27,7 +27,7 @@ nav:
       - Introduction: graphbin2_intro.md
       - Preprocess: graphbin2_preprocess.md
       - Usage: graphbin2_usage.md
-    - Support:
+    - Processing:
       - Prepare: prepare.md
       - Visualise: visualise.md
       - Evaluate: evaluate.md