Merge pull request #29 from genotoul-bioinfo/dev

Add citation section with joss paper

README.md

@@ -28,9 +28,9 @@ Binette is inspired from the metaWRAP bin-refinement tool but it effectively sol
 
 A comprehensive documentation of Binette is avalaible here: https://binette.readthedocs.io/
 
-# Installation
+## Installation
 
-## With Bioconda
+### With Bioconda
 
 Binette can be easilly installed with conda 
 
@@ -46,7 +46,7 @@ binette -h
 ```
 
 
-## From a conda environnement
+### From a conda environnement
 
 Clone this repository: 
 ```
@@ -73,7 +73,7 @@ binette -h
 ```
 
 
-## Downloading the CheckM2 database
+### Downloading the CheckM2 database
 
 Before using Binette, it is necessary to download the CheckM2 database:
 
@@ -84,9 +84,9 @@ checkm2 database --download --path <checkm2/database/>
 Make sure to replace `<checkm2/database/>` with the desired path where you want to store the CheckM2 database.
 
 
-# Usage 
+## Usage 
 
-## Input Formats
+### Input Formats
 
 Binette supports two input formats for bin sets: 
 
@@ -143,7 +143,7 @@ For example, consider the following two `contig2bin_tables`:
 
 In both formats, the `--contigs` argument should specify a FASTA file containing all the contigs found in the bins. Typically, this file would be the assembly FASTA file used to generate the bins. In these exemple the `assembly.fasta` file should contain at least the five contigs mentioned in the `contig2bin_tables` files or in the bin fasta files: `contig_1`, `contig_8`, `contig_15`, `contig_9`, and `contig_10`.
 
-## Outputs
+### Outputs
 
 Binette results are stored in the `results` directory. You can specify a different directory using the `--outdir` option.
 
@@ -167,12 +167,19 @@ The `final_bins_quality_reports.tsv` file contains the following columns:
 | **N50**             | Displays the N50 of the bin.                                                                                |
 | **contig_count**    | The number of contigs contained within the bin.                                                             |
 
-# Help, feature requests and bug reporting
+## Help, feature requests and bug reporting
 
 To report bugs, request new features, or seek help and support, please open an [issue](https://github.com/genotoul-bioinfo/Binette/issues). 
 
 
-# Licence
+## Licence
 
 This program is released as an open source software under the terms of [MIT License](LICENSE).
 
+
+## Citations
+
+Binette is scientific software, with a [published paper](https://joss.theoj.org/papers/10.21105/joss.06782) in the [Journal of Open-Source Software](https://joss.theoj.org/). 
+If you use Binette in academic research, please cite the following paper:
+
+> Mainguy et al., (2024). Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes.. Journal of Open Source Software, 9(102), 6782, https://doi.org/10.21105/joss.06782