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Part 1: Document Description
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Citation |
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Title: |
Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes |
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Identification Number: |
doi:10.23708/RJDLCN |
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Distributor: |
DataSuds |
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Date of Distribution: |
2022-08-18 |
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Version: |
1 |
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Bibliographic Citation: |
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 |
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Citation |
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Title: |
Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes |
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Identification Number: |
doi:10.23708/RJDLCN |
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Authoring Entity: |
Orjuela, Julie (UMR DIADE - IRD, University of Montpellier, CIRAD - France) |
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Comte, Aurore (UMR PHIM - IRD, University of Montpellier, CIRAD, INRAe, Agro Institut - France) |
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Ravel, Sébastien (UMR PHIM - CIRAD, University of Montpellier, IRD, INRAe, Agro Institut - France) |
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Charriat, Florian (UMR PHIM - INRAe, University of Montpellier, IRD, CIRAD, Agro Institut - France) |
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Vi, Tram (UMR DIADE - IRD, University of Montpellier, CIRAD - France) |
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Sabot, Francois (UMR DIADE - IRD, University of Montpellier, CIRAD - France) |
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Cunnac, Sébastien (UMR PHIM - IRD, University of Montpellier, CIRAD, INRAe, Agro Institut - France) |
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Software used in Production: |
culebrONT |
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Grant Number: |
MagMAX ANR-18-CE20-0016 grant awarded to Pierre Gladieux |
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Grant Number: |
MagMAX ANR-18-CE20-0016 grant awarded to Pierre Gladieux |
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Distributor: |
DataSuds |
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Access Authority: |
Orjuela, Julie |
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Depositor: |
Orjuela, Julie |
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Date of Deposit: |
2022-08-17 |
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Holdings Information: |
https://doi.org/10.23708/RJDLCN |
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Study Scope |
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Keywords: |
Computer and Information Science, assembly, quality control, long reads, FAIR, reproducibility, snakemake pipeline, python package, genome |
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Topic Classification: |
Computer sciences |
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Abstract: |
Related to CulebrONT software, this dataset includes: <b><br>- data used to test the software <br>- 2 reports generated by the software : from the test data and from other data <br>- supplementary technical information about CulebrONT pipeline</b> |
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Notes: |
<b>CulebrONT</b> 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. <br>Documentation: <a href="https://culebront-pipeline.readthedocs.io/en/2.1.1/">https://culebront-pipeline.readthedocs.io/en/2.1.1/</a> <br>Code development: <a href="https://github.com/SouthGreenPlatform/culebrONT">https://github.com/SouthGreenPlatform/culebrONT</a> <br> <a href="https://southgreenplatform.github.io/trainings/contact/"><img src="https://southgreenplatform.github.io/tutorials/images/southgreenlong.png" width=120></a><br> The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work. |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Materials |
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<a href="https://culebront-pipeline.readthedocs.io/en/2.1.1/">https://culebront-pipeline.readthedocs.io/en/2.1.1/</a> |
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<a href="https://github.com/SouthGreenPlatform/culebrONT">https://github.com/SouthGreenPlatform/culebrONT</a> |
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Related Publications |
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Citation |
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Title: |
Orjuela, J. et al. (2022) « Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes ». DataSuds. doi:10.23708/TBPNWJ.<br> |
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Identification Number: |
10.23708/tbpnwj |
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Bibliographic Citation: |
Orjuela, J. et al. (2022) « Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes ». DataSuds. doi:10.23708/TBPNWJ.<br> |
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Citation |
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Title: |
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 |
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Identification Number: |
10.1101/2021.07.19.452922 |
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Bibliographic Citation: |
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 |
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Label: |
CulebrONT_Data-Xoo-sub.zip |
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Text: |
Dataset used to test CulebrONT code |
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Notes: |
application/zip |
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Label: |
CulebrONT_PCJ_supplemental.pdf |
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Text: |
Supplementary information related to CulebrONT pipeline implementation |
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Notes: |
application/pdf |
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Label: |
CulebrONT_REPORTS.zip |
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Text: |
Reports generated by the CulebrONT software with data from different organisms (rice, nematoda, bacteria) as described in the PCJ manuscript |
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Notes: |
application/zip |
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Label: |
CulebrONT_REPORT_Data-Xoo-sub.zip |
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Text: |
Final report generated by CulebrONT software using the test dataset Data-Xoo-sub.zip |
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Notes: |
application/zip |