From 113d7bf1fec2243e4747b48959acdc82f4e8edfa Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Fri, 20 Sep 2024 15:39:01 +0930 Subject: [PATCH 1/3] DOC: update README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 852767c..046a42e 100644 --- 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.

Initial binning From cd4fad1ea4ded7d4116d442c5302f6b06aab7993 Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Fri, 20 Sep 2024 15:41:27 +0930 Subject: [PATCH 2/3] DOC: update docs --- docs/graphbin2_preprocess.md | 2 +- docs/index.md | 2 +- mkdocs.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/graphbin2_preprocess.md b/docs/graphbin2_preprocess.md index 38629a0..0752d4c 100644 --- 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 index 4bfb82d..91ff58d 100644 --- 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 index 82bd9c2..70a4cd2 100644 --- 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 \ No newline at end of file From 6cb522ef8f43cb1e93d53ead04e977e3678b9953 Mon Sep 17 00:00:00 2001 From: Vijini Mallawaarachchi Date: Fri, 20 Sep 2024 15:43:11 +0930 Subject: [PATCH 3/3] DOC: update docs --- docs/evaluate.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/evaluate.md b/docs/evaluate.md index 91cbcd9..9a89579 100644 --- 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)