DIversity - Adaptation - plant DEvelopment

The DIADE Research Unit aims to understand the diversification of tropical plants, one of the main original reservoirs of biodiversity, and for which conservation, management and exploitation are an important issue for Sustainable Development.

The nine teams forming the Unit belong to IRD, University of Montpellier, CIRAD, and CNRS.
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Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Aug 18, 2022
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
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: h...
culebrONT-2.1.1.tar.gz
Aug 18, 2022 - Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Gzip Archive - 829.1 KB - MD5: c9d6c534f6cbdcb0de33a79b1a1a51c0
Code
Source code of culebrONT pipeline stable version 2.1.1
Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Aug 18, 2022
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
Related to CulebrONT software, this dataset includes: - data used to test the software - 2 reports generated by the software : from the test data and from other data - supplementary technical information about CulebrONT pipeline
CulebrONT_Data-Xoo-sub.zip
Aug 18, 2022 - Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
ZIP Archive - 314.2 MB - MD5: c1d4d4fb38546ad3e07c34c25203ab73
Data
Dataset used to test CulebrONT code
CulebrONT_PCJ_supplemental.pdf
CulebrONT_PCJ_supplemental.pdf
Aug 18, 2022 - Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
Adobe PDF - 1.1 MB - MD5: 491db3bc9c1d44f16d9eb0a4ce2f4c43
Documentation
Supplementary information related to CulebrONT pipeline implementation
CulebrONT_REPORT_Data-Xoo-sub.zip
Aug 18, 2022 - Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
ZIP Archive - 27.0 MB - MD5: 063d9231f2ccd8e571191ab2c2ef503d
DataDocumentation
Final report generated by CulebrONT software using the test dataset Data-Xoo-sub.zip
CulebrONT_REPORTS.zip
Aug 18, 2022 - Test data, reports and documentation for CulebrONT software: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes
ZIP Archive - 813.6 MB - MD5: 595aa262a2ffcd91fb88d785cd3fa4dc
DataDocumentation
Reports generated by the CulebrONT software with data from different organisms (rice, nematoda, bacteria) as described in the PCJ manuscript
DYNADIV Team(UMR DIADE)
DYNADIV Team logo
Jun 9, 2022
The main focus of DYNADIV Team is tounderstand how biodiversity of tropical plants is shaped through evolutionary forces resulting from human and environmental impacts. Its activity is essentially based on population genetics but also integrates a multidisciplinary approach inclu...
Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning
Feb 1, 2021 - EVOGEC Team
Guyot, Romain; Orozco-Arias, Simon; Isaza, Gustavo, 2021, "Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning", https://doi.org/10.23708/QCMOUA, DataSuds, V2
Here, we present InpactorDB a semi-curated dataset composed of 130,511 elements from 195 plant genomes belonging to 108 plant species, classified down to the lineage level. This dataset has been used to train two deep neural networks (one fully connected and one convolutional) fo...
InpactorDB_non-redundant_V2.format.fasta
Feb 1, 2021 - Fasta files for InpactorDB: A Plant classified lineage-level LTR retrotransposon reference library for free-alignment methods based on Machine Learning
Unknown - 564.5 MB - MD5: e7d6bb2820ebf82252f7f39a4f583641
Data
Fasta file for InpactorDB V2. NON-redundant database of LTR retrotransposons.
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