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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.

## Available commands

Run `gbintk --help` or `gbintk -h` to list the help message for GraphBin-Tk.

```bash
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
```

### `gbintk graphbin`: Run [GraphBin](https://github.com/metagentools/GraphBin)
<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">
</p>

Run `gbintk graphbin --help` or `gbintk graphbin -h` to list the help message for GraphBin.
## Installing GraphBin-Tk

You can clone the `gbintk` repository to your machine.
```shell
Usage: gbintk graphbin [OPTIONS]

GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs

Options:
--assembler [spades|megahit|flye]
name of the assembler used (SPAdes, MEGAHIT
or Flye) [required]
--graph PATH path to the assembly graph file [required]
--contigs PATH path to the contigs file [required]
--paths PATH path to the contigs.paths (metaSPAdes) or
assembly.info (metaFlye) file
--binned PATH path to the .csv file with the initial
binning output from an existing tool
[required]
--output PATH path to the output folder [required]
--prefix TEXT prefix for the output file
--max_iteration INTEGER maximum number of iterations for label
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: ,]
-h, --help Show this message and exit.
git clone https://github.com/metagentools/gbintk.git
```

### `gbintk graphbin2`: Run [GraphBin2](https://github.com/metagentools/GraphBin2)

Run `gbintk graphbin2 --help` or `gbintk graphbin2 -h` to list the help message for GraphBin2.

Now go into the `gbintk` folder using the following command.
```shell
Usage: gbintk graphbin2 [OPTIONS]

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using
Assembly Graphs

Options:
--assembler [spades|megahit|flye]
name of the assembler used (SPAdes, MEGAHIT
or Flye) [required]
--graph PATH path to the assembly graph file [required]
--contigs PATH path to the contigs file [required]
--paths PATH path to the contigs.paths (metaSPAdes) or
assembly.info (metaFlye) file
--abundance PATH path to the abundance file [required]
--binned PATH path to the .csv file with the initial
binning output from an existing tool
[required]
--output PATH path to the output folder [required]
--prefix TEXT prefix for the output file
--depthb INTEGER maximum depth for the breadth-first-search.
[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: ,]
--nthreads INTEGER number of threads to use. [default: 8]
-h, --help Show this message and exit.
cd gbintk
```

### `gbintk metacoag`: Run [MetaCoAG](https://github.com/metagentools/MetaCoAG)

Run `gbintk metacoag --help` or `gbintk metacoag -h` to list the help message for MetaCoAG.
Once you have installed `conda`, make sure you are in the `gbintk` folder. Now run the following commands to create a conda environment and activate it to run `gbintk`.

```shell
Usage: gbintk metacoag [OPTIONS]

MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly
Graphs

Options:
--assembler [spades|megahit|flye]
name of the assembler used (SPAdes, MEGAHIT
or Flye) [required]
--graph PATH path to the assembly graph file [required]
--contigs PATH path to the contigs file [required]
--paths PATH path to the contigs.paths (metaSPAdes) or
assembly.info (metaFlye) file
--abundance PATH path to the abundance file [required]
--output PATH path to the output folder [required]
--hmm TEXT path to marker.hmm file. [default:
auxiliary/marker.hmm]
--prefix TEXT prefix for the output file
--min_length INTEGER minimum length of contigs to consider for
binning. [default: 1000]
--p_intra FLOAT RANGE minimum probability of an edge matching to
assign to the same bin. [default: 0.1;
0<=x<=1]
--p_inter FLOAT RANGE maximum probability of an edge matching to
create a new bin. [default: 0.01; 0<=x<=1]
--d_limit INTEGER distance limit for contig matching.
[default: 20]
--depthlp INTEGER depth to consider for label propagation.
[default: 10]
--n_mg INTEGER total number of marker genes. [default:
108]
--no_cut_tc do not use --cut_tc for hmmsearch.
--mg_threshold FLOAT RANGE length threshold to consider marker genes.
[default: 0.5; 0<=x<=1]
--bin_mg_threshold FLOAT RANGE minimum fraction of marker genes that should
be present in a bin. [default: 0.33333;
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: ,]
--nthreads INTEGER number of threads to use. [default: 8]
-h, --help Show this message and exit.
conda env create -f environment.yml
conda activate gbintk
```

### `gbintk prepare`: Format the initial binning result from an existing binning tool

Run `gbintk prepare --help` or `gbintk prepare -h` to list the help message for formatting.
You ca run the following command to install `gbintk` using `flit`.

```shell
Usage: gbintk prepare [OPTIONS]

Format the initial binning result from an existing binning tool

Options:
--assembler [spades|megahit|flye]
name of the assembler used (SPAdes, MEGAHIT
or Flye) [required]
--resfolder PATH path to the folder containing FASTA files
for individual bins [required]
--delimiter [,|;| |" "] delimiter for input/output results. Supports
a comma (,), a semicolon (;), a tab ($'\t'),
a space (" ") and a pipe (|) [default: ,]
--prefix TEXT prefix for the output file
--output PATH path to the output folder [required]
-h, --help Show this message and exit.
flit install
```

### `gbintk visualise`: Visualise binning and refinement results

Run `gbintk visualise --help` or `gbintk visualise -h` to list the help message for visualisation.
Now run the following command to ensure that `gbintk` is working.

```shell
Usage: gbintk visualise [OPTIONS]

Visualise binning and refinement results

Options:
--assembler [spades|megahit|flye]
name of the assembler used (SPAdes, MEGAHIT
or Flye) [required]
--initial PATH path to the initial binning result
[required]
--final PATH path to the final binning result [required]
--graph PATH path to the assembly graph file [required]
--paths PATH path to the contigs.paths (metaSPAdes) or
assembly.info (metaFlye) file
--output PATH path to the output folder [required]
--prefix TEXT prefix for the output file
--dpi INTEGER dpi value [default: 300]
--width INTEGER width of the image in pixels [default:
2000]
--height INTEGER height of the image in pixels [default:
2000]
--vsize INTEGER size of the vertices [default: 50]
--lsize INTEGER size of the vertex labels [default: 8]
--margin INTEGER margin of the figure [default: 50]
--type TEXT type of the image (jpg, png, eps, svg)
[default: png]
--delimiter [,|;|$'\t'|" "] delimiter for input/output results. Supports
a comma (,), a semicolon (;), a tab ($'\t'),
a space (" ") and a pipe (|) [default: ,]
-h, --help Show this message and exit.
gbintk --help
```

### `gbintk evaluate`: Evaluate binning results give a ground trith
## Available commands in GraphBin-Tk

Run `gbintk evaluate --help` or `gbintk evaluate -h` to list the help message for evaluation.
Run `gbintk --help` or `gbintk -h` to list the help message for GraphBin-Tk.

```shell
Usage: gbintk evaluate [OPTIONS]
Usage: gbintk [OPTIONS] COMMAND [ARGS]...

Evaluate the binning results given a ground truth
gbintk (GraphBin-Tk): Assembly graph-based metagenomic binning toolkit

Options:
--binned PATH path to the .csv file with the initial binning
output from an existing tool [required]
--groundtruth PATH path to the .csv file with the ground truth
[required]
--delimiter [,|;| |" "] delimiter for input/output results. Supports a
comma (,), a semicolon (;), a tab ($'\t'), a space
(" ") and a pipe (|) [default: ,]
--output PATH path to the output folder [required]
-h, --help Show this message and exit.
-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
```

**Detailed documentation hosted at [Read the Docs](https://gbintk.readthedocs.io/en/latest/) is coming soon!**

## Citation

If you use GraphBin-Tk in your work, please cite the relevant tools.
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