Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Version 3.0

Orjuela, Julie; Comte, Aurore; Ravel, Sébastien; Charriat, Florian; Vi, Tram; Sabot, François; Cunnac, Sébastien, 2022, "Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes", https://doi.org/10.23708/TBPNWJ, DataSuds, V3

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Description	CulebrONT is an open-source, scalable, modulable and traceable snakemake pipeline, able to launch multiple assembly tools in parallel and providing help for choosing the best possible assembly. Documentation: https://culebront-pipeline.readthedocs.io/en/2.1.1/ Code development: https://github.com/SouthGreenPlatform/culebrONT The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work.
Subject	Computer and Information Science
Keyword	assembly, quality control, long reads, FAIR, reproducibility, snakemake pipeline, python package, genome
Related Publication	Julie Orjuela, Aurore Comte, Sébastien Ravel, Florian Charriat, Tram Vi, François Sabot, Sébastien Cunnac. CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes. https://www.biorxiv.org/content/10.1101/2021.07.19.452922v2 doi: 10.1101/2021.07.19.452922

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	culebrONT-2.1.1.tar.gz Gzip Archive - 829.1 KB Published Aug 18, 2022 2 Downloads MD5: c9d6c534f6cbdcb0de33a79b1a1a51c0 Source code of culebrONT pipeline stable version 2.1.1 Code	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX

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Dataset Persistent ID	doi:10.23708/TBPNWJ
Publication Date	2022-03-08
Title	Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Alternative URL	https://culebront-pipeline.readthedocs.io/en/2.1.1/
Other ID	Bioversity, CIRAD, INRAe, IRD: South Green platform https://southgreenplatform.github.io/trainings/contact/ IFB - French Institut of Bioinformatics
Author	Orjuela, Julie (UMR DIADE - IRD, University of Montpellier, CIRAD - France) - ORCID: 0000-0001-8387-2266 Comte, Aurore (UMR PHIM - IRD, University of Montpellier, CIRAD, INRAe, Agro Institut - France) - ORCID: 0000-0002-6891-5739 Ravel, Sébastien (UMR PHIM - CIRAD, University of Montpellier, IRD, INRAe, Agro Institut - France) - ORCID: 0000-0001-6663-782X Charriat, Florian (UMR PHIM - INRAe, University of Montpellier, IRD, CIRAD, Agro Institut - France) - ORCID: 0000-0001-9485-4119 Vi, Tram (UMR DIADE - IRD, University of Montpellier, CIRAD - France) 0000-0002-4319-5544 Sabot, François (UMR DIADE - IRD, University of Montpellier, CIRAD - France) - ORCID: 0000-0002-8522-7583 Cunnac, Sébastien (UMR PHIM - IRD, University of Montpellier, CIRAD, INRAe, Agro Institut - France) - ORCID: 0000-0002-3695-491X
Contact	Use email button above to contact. Orjuela, Julie (UMR DIADE - IRD, University of Montpellier, CIRAD - France)
Description	CulebrONT is an open-source, scalable, modulable and traceable snakemake pipeline, able to launch multiple assembly tools in parallel and providing help for choosing the best possible assembly. Documentation: https://culebront-pipeline.readthedocs.io/en/2.1.1/ Code development: https://github.com/SouthGreenPlatform/culebrONT The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work.
Subject	Computer and Information Science
Keyword	assembly quality control long reads FAIR reproducibility snakemake pipeline python package genome
Scientific Theme	Computer science (NumeriSud) https://numerisud.ird.fr/documents-et-films/(thematique)/G%C3%A9n%C3%A9ralit%C3%A9s+/+Sciences+fondamentales+et+techniques_Informatique
Related Publication	Julie Orjuela, Aurore Comte, Sébastien Ravel, Florian Charriat, Tram Vi, François Sabot, Sébastien Cunnac. CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes. https://www.biorxiv.org/content/10.1101/2021.07.19.452922v2 doi: 10.1101/2021.07.19.452922 https://doi.org/10.1101/2021.07.19.452922 Orjuela, Julie; Comte, Aurore; Ravel, Sébastien; Charriat, Florian; Vi, Tram; Sabot, Francois; Cunnac, Sébastien, 2022, "Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes", https://doi.org/10.23708/RJDLCN, DataSuds, V1 doi: 10.23708/rjdlcn https://doi.org/10.23708/rjdlcn
Language	English
Grant Information	IRD engineer and research permanent positions DIADE and PHIM research units CIRAD engineer permanent positions PHIM research unit IRD engineer contract PHIM research unit INRAe engineer contract PHIM research unit: MagMAX ANR-18-CE20-0016 grant awarded to Pierre Gladieux. IRD engineer contract by PHIM funding and the CRP-Rice program
Depositor	Orjuela, Julie
Deposit Date	2022-02-28
Kind of Data	code data
Software	culebrONT, Version: 2.1.1
Related Material	https://culebront-pipeline.readthedocs.io/en/2.1.1/; https://github.com/SouthGreenPlatform/culebrONT

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