diff --git a/README.md b/README.md index c565815..5b73523 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,8 @@ -# ConDiGA +
+ +
+ +# ConDiGA: Contigs Directed Gene Annotation [![DOI](https://img.shields.io/badge/Preprint_DOI-10.1101/2023.04.19.537311-blue)](https://doi.org/10.1101/2023.04.19.537311) [![DOI](https://zenodo.org/badge/531343291.svg)](https://zenodo.org/badge/latestdoi/531343291) @@ -149,6 +153,11 @@ The output of ConDiGA will contain the following main files and folders. * `all_genes.output` contains `minimap2` mapping results for the predicted genes * `Assemblies` contains FASTA files of the downloaded reference genomes +# Acknowledgement + +The ConDiGA logo was generated using [DALLĀ·E 3](https://openai.com/dall-e-3) from [OpenAI](https://openai.com/) with the following prompt. +> Create an icon that visually represents the concept of contigs directed gene annotation for a tool logo ensuring the background is completely transparent. + ## Citation ConDiGA has been accepted for publication at [Microbiome](https://microbiomejournal.biomedcentral.com/). Stay tuned for the Microbiome publication. @@ -171,3 +180,9 @@ If you use ConDiGA in your work, please cite the [bioRxiv preprint](https://www. ``` **NOTE:** The database created by ConDiGA is described as MD3 in the manuscript. + +Also, please cite the following tools/databases used by ConDiGA. + +* Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic acids research, 38 (12): 132-132 (2010). [https://doi.org/10.1093/nar/gkq275] (https://doi.org/10.1093/nar/gkq275) +* Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100 (2018). [https://doi.org/10.1093/bioinformatics/bty191](https://doi.org/10.1093/bioinformatics/bty191) +* Woodcroft BJ, Newell R, CoverM: Read coverage calculator for metagenomics (2017). [https://github.com/wwood/CoverM](https://github.com/wwood/CoverM) \ No newline at end of file