
![pips](https://github.com/Lcornet/GENERA/blob/main/images/GENERA-pips.png)

# BCCM GEN-ERA tools repository

Please visit the wiki for tutorials and access to the tools:
https://github.com/Lcornet/GENERA/wiki  

# NEWS
Mantis is now installed in a singularity container for the Metabolic workflow (install is no longer necessary).  

# Information about the GEN-ERA project
Please visit  
https://bccm.belspo.be/content/bccm-collections-genomic-era  

# Publications
1. ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies.  
   Léonard, R. R., Leleu, M., Vlierberghe, M. V., Cornet, L., Kerff, F., and Baurain, D. (2021).  
   PeerJ 9, e11348. doi:10.7717/peerj.11348.  
   https://peerj.com/articles/11348/  
2. The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach.  
   Cornet, L., D’hooge, E., Magain, N., Stubbe, D., Packeu, A., Baurain, D., and Becker P. (2021).  
   Microbial Genomics 7, 000707. doi:10.1099/mgen.0.000707.  
   https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000707  
3. ORPER: A Workflow for Constrained SSU rRNA Phylogenies.  
   Cornet, L., Ahn, A.-C., Wilmotte, A., and Baurain, D. (2021).  
   Genes 12, 1741. doi:10.3390/genes12111741.  
   https://www.mdpi.com/2073-4425/12/11/1741/html  
4. AMAW: automated gene annotation for non-model eukaryotic genomes.  
   Meunier, L., Baurain, D., Cornet, L. (2021)  
   https://www.biorxiv.org/content/10.1101/2021.12.07.471566v1  
5. Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveals taxonomic and functional diversity.  
   Cornet, L.,  Cleenwerck, I., Praet, J., Leonard, R., Vereecken, N.J., Michez, D., Smagghe, G., Baurain, D., Vandamme, P. (2021)  
   https://www.biorxiv.org/content/10.1101/2021.12.10.472130v1  
6. Contamination detection in genomic data: more is not enough.   
   Cornet, L & Baurain, D (2022)   
   Genome Biology. 2022;23:60.  
   https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02619-9  
7. The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics  
   Cornet, L., Durieu, B., Baert, F., D’hooge, E., Colignon, D., Meunier, L., Lupo, V., Cleenwerck I.,
   Daniel, HM., Rigouts, L., Sirjacobs, D., Declerck, D., Vandamme, P., Wilmotte, A., Baurain, D., Becker P (2022).  
   https://www.biorxiv.org/content/10.1101/2022.10.20.513017v1  
8. CRitical Assessment of genomic COntamination detection at several Taxonomic ranks (CRACOT)    
   Cornet, L., Lupo, V., Declerck, S., Baurain, D. (2022).   
   https://www.biorxiv.org/content/10.1101/2022.11.14.516442v1  

# Copyright and License

This softwares is copyright (c) 2017-2021 by University of Liege / Sciensano / BCCM collection by Luc CORNET
This is free softwares; you can redistribute it and/or modify.

![BCCM](https://github.com/Lcornet/GENERA/blob/main/images/GENERA-logo.png)  
