EuGene: integrative gene finder for eukaryotic and prokaryotic genomes

Download

• Eukaryote EuGene pipeline - Version 1.6.5 (2021-07-05) egnep-Linux-x86_64.1.6.5.tar.gz
• Prokaryote EuGene pipeline - Version 1.3 (2019-02-01) egnpp-Linux-x86_64.1.3.tar.gz
• EuGene C++ programs:
  • Version 4.3 eugene-4.3.tar.gz (Note#1: use g++-5 to compile. #2: compiling documentation requires pdflatex found in texlive-latex-base debian package)
  • Version 5.0.0 eugene-v5.0.0.tar.gz changelog
• Eugene's environment requirements (configs and models), these have to be put in the EUGENE_DEFAULT_DIR:
  • Base environment (contains cfg/ and models/ directories): egn-base-environment.tar.gz
  • Available eukaryote Weight Array Models (to put in models/WAM): WAM
• Eugene Singularity/Apptainer container (including environments and WAM files):
  • EuGene 4.3: eugene-4.3.sif SHA256
  • EuGene v5.0.0: eugene-v5.0.0.sif SHA256
• Eukaryote EuGene pipeline - Version 2 (Nextflow/Singularity based)
  • Version 2.0.4 (2023-01-24) egnep-nextflow-2.0.4.tar.gz
  • Version 2.1.0 (Masked Genomes management, Miniprot as default for DB reduction ) (2023-03-03) egnep-nextflow-2.1.0.tar.gz
  • Version 2.1.1 (Add possibility to overwrite EuGene Sensor Plugin templates) (2023-09-21) egnep-nextflow-2.1.1.tar.gz

Documentation

• EuGene Reference protocol: Sallet E., Gouzy J., Schiex T. (2019) EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes. Methods in Molecular Biology
• EuGene C++ program documentation: EuGeneDoc.pdf

To cite EuGene

Sallet E., Gouzy J., Schiex T. (2019) EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes. Methods in Molecular Biology

References

Sallet E., Gouzy J., Schiex T. (2014) EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes. Bioinformatics

Sallet E. et al (2013) Next-generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011. DNA Research

Foissac S., Gouzy J., Rombauts S. et al (2008) Genome annotation in plants and fungi: EuGène as a model platform Curr. Bioinformatics

Foissac S., Schiex T. (2005) Integrating alternative splicing detection into gene prediction BMC Bioinformatics

Foissac S., Bardou P., Moisan A., Cros MJ., Schiex T. (2003) EuGene'Hom: a generic similarity-based gene finder using multiple homologuous sequences. Nucleic Acid Res., vol. 31, n. 13

References using EuGene

• Rich M., Vigneron N.et al (2021) Lipid exchanges drove the evolution of mutualism during plant terrestrialization Science
• Nicoud Q.et al (2021) Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency mSystems
• Badouin H.et al (2020) The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication Genome Biology
• Hufnagel B.et al (2020) High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nature Communications
• Raymond O.et al (2018) The Rosa genome provides new insights into the domestication of modern roses Nature Genetics
• Pecrix Y, Staton E, Sallet E et al (2018) Whole-genome landscape of Medicago truncatula symbiotic genes. Nature Plants
• Daccord N.et al (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development Nature Genetics
• Badouin H.et al (2017) The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution Nature
• Arnaiz O. et al (2017) Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. BMC Genomics
• Blanc-Mathieu R. et al (2017) Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLOS Genetics
• Ropars J. et al (2015) Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Current biology
• Cheeseman K.et al (2014) Multiple recent horizontal transfers of a large genomic region in cheese making fungi Nature communications
• The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution Nature
• Young N. D. et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses Nature
• Argout X. et al (2011) The genome of Theobroma cacao Nature genetics
• Abad P.et al (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nature biotechnology

Contact

For questions, bug reports, contact the EuGene team: eugene-help@groupes.renater.fr
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