The GEN-ERA toolbox is a suite of Nextflow-Singularity workflows designed for comparative genomics of bacteria and small eukaryotes. Without any installation, it allows researchers to download, assemble and bin (meta)genomes (from short or long reads). Orthologous inference and maximum likelihood phylogenomic analyses (bootstrap and jackknife) can be inferred with this suite. Constrained (by a ribosomal phylogenomic) SSU rRNA phylogeny can also be inferred. Average nucleotide identity, GTDB identification and metabolic modelling are also included in the toolbox.
Please visit the wiki for tutorials and access to the tools: https://github.com/Lcornet/GENERA/wiki
Assembly V3.0.0 is available - Major update - March 27 2024.
- Possibility to use only long reads
- add skiptrimming option
- add skippolishing option
- add binningmethod option
- add LRbinnier in binner
- delete quast, please use GENcontams instead
- genomeSIZE option now only used for CANU
Please visit
https://bccm.belspo.be/content/bccm-collections-genomic-era
Pierre Becker, Luc Cornet, Elizabet D’hooge, Ilse Cleenwerck, Oren Tzfadia, Leen Rigouts, Wim Mulders, Heide-Marie Daniel, Annick Wilmotte, Denis Baurain. BCCM collections in the genomic era. Final Report.
Brussels: Belgian Science PolicyOffice2022–40p. (BRAIN-be2.0-(Belgian Research Action through Interdisciplinary Networks))
https://www.belspo.be/belspo/brain2-be/projects/FinalReports/BCCMGENERA_FinRep.pdf
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.
