UMR DIADE

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.

CERES Team

DYNADIV Team

EVOGEC Team

ADvENS Team

AgroLD

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1 to 10 of 996 Results

GrAnnoT source code and scripts Mar 20, 2025 - GrAnnoT Sabot, Francois; Marthe, Nina; Zytnicki, Matthias, 2025, "GrAnnoT source code and scripts", https://doi.org/10.23708/TW3KYV, DataSuds, V2 GrAnnoT is an annotation transfer tool for pangenome graph. The source code at the time of the paper submission is available in this dataset. The git repository is available at : https://forge.ird.fr/diade/dynadiv/grannot/-/tree/main
ReadMe.txt Mar 20, 2025 - GrAnnoT source code and scripts Plain Text - 516 B - MD5: 25f858eade603eac11fdeab6de8f5863 Documentation Data citation, description and terms of use
Output from the analysis described in GrAnnoT paper Mar 20, 2025 - GrAnnoT data and output Marthe, Nina; Sabot, Francois, 2025, "Output from the analysis described in GrAnnoT paper", https://doi.org/10.23708/RRSKRA, DataSuds, V5 GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the outputs from these tests are available in this dataset. It includes mainly transferred annotations.
ReadMe.txt Mar 20, 2025 - Output from the analysis described in GrAnnoT paper Plain Text - 499 B - MD5: 683ef0fb3b9ffa3088f3c14f327409b3 Documentation Data citation, description and terms of use
Data used for the analysis described in GrAnnoT paper Mar 20, 2025 - GrAnnoT data and output Marthe, Nina; Sabot, Francois, 2025, "Data used for the analysis described in GrAnnoT paper", https://doi.org/10.23708/DO1RTF, DataSuds, V5 GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the data necessary for these tests is available in this dataset. It includes mainly pangenome graphs, genomes, and annotations.
ReadMe.txt Mar 20, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 488 B - MD5: e92eb31e2015df3e015c0b4f9fec78b2 Documentation Data citation, description and terms of use
HumanChr1Graph_renamePaths.gfa Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 4.5 GB - MD5: 1db6205a09ea265f3385744974113906 Data Human chromosome 1 pangenome graph made by the Human Pangenome Reference Consortium, and available at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/scratch/2022_03_11_minigraph_cactus/.
RiceGraph_MGC.gfa Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 4.1 GB - MD5: 17cccb331973224bd4073066369cf1f2 Data Asian rice pangenome graph built with the Nipponbare genome from the paper from 2020 by Zhou, Y., Chebotarov, D., Kudrna, D. et al., "A platinum standard pan-genome resource that represents the population structure of Asian rice" (doi:10.1038/s41597-020-0438-2), and 12 other gen...
RiceGraph_MGC_paths.gfa Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 4.3 GB - MD5: f541072bfc36b01c4bb1609192c272b9 Data Pangenome graph adapted from the file "RiceGraph_MGC.gfa" by converting the walks into paths.
RiceGraph_MGC_refOs127652RS1.gfa Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 4.6 GB - MD5: e58d668a5ea6a6a2f2c8033032adcfb4 Data Pangenome graph built with the same data as the file "RiceGraph_MGC.gfa", but with a different genome used as reference (Os127652RS1).

GrAnnoT source code and scripts

Mar 20, 2025 - GrAnnoT

Sabot, Francois; Marthe, Nina; Zytnicki, Matthias, 2025, "GrAnnoT source code and scripts", https://doi.org/10.23708/TW3KYV, DataSuds, V2

GrAnnoT is an annotation transfer tool for pangenome graph. The source code at the time of the paper submission is available in this dataset. The git repository is available at : https://forge.ird.fr/diade/dynadiv/grannot/-/tree/main

ReadMe.txt

Mar 20, 2025 - GrAnnoT source code and scripts

Plain Text - 516 B -

Documentation

Data citation, description and terms of use

Output from the analysis described in GrAnnoT paper

Mar 20, 2025 - GrAnnoT data and output

Marthe, Nina; Sabot, Francois, 2025, "Output from the analysis described in GrAnnoT paper", https://doi.org/10.23708/RRSKRA, DataSuds, V5

GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the outputs from these tests are available in this dataset. It includes mainly transferred annotations.

ReadMe.txt

Mar 20, 2025 - Output from the analysis described in GrAnnoT paper

Plain Text - 499 B -

Documentation

Data citation, description and terms of use

Data used for the analysis described in GrAnnoT paper

Mar 20, 2025 - GrAnnoT data and output

Marthe, Nina; Sabot, Francois, 2025, "Data used for the analysis described in GrAnnoT paper", https://doi.org/10.23708/DO1RTF, DataSuds, V5

GrAnnoT is an annotation transfer tool for pangenome graph. It was tested and compared to other approaches, and the data necessary for these tests is available in this dataset. It includes mainly pangenome graphs, genomes, and annotations.

ReadMe.txt

Mar 20, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 488 B -

Documentation

Data citation, description and terms of use

HumanChr1Graph_renamePaths.gfa

Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 4.5 GB -

Data

Human chromosome 1 pangenome graph made by the Human Pangenome Reference Consortium, and available at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/scratch/2022_03_11_minigraph_cactus/.

RiceGraph_MGC.gfa

Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 4.1 GB -

Data

Asian rice pangenome graph built with the Nipponbare genome from the paper from 2020 by Zhou, Y., Chebotarov, D., Kudrna, D. et al., "A platinum standard pan-genome resource that represents the population structure of Asian rice" (doi:10.1038/s41597-020-0438-2), and 12 other gen...

RiceGraph_MGC_paths.gfa

Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 4.3 GB -

Data

Pangenome graph adapted from the file "RiceGraph_MGC.gfa" by converting the walks into paths.

RiceGraph_MGC_refOs127652RS1.gfa

Mar 18, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 4.6 GB -

Data

Pangenome graph built with the same data as the file "RiceGraph_MGC.gfa", but with a different genome used as reference (Os127652RS1).

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