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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21 to 30 of 962 Results

nb_allFeatures_renamed_filter.bed Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper PLINK Binary - 92.5 MB - MD5: 09bb2ab302dd81c51549bff1a2e4116e Data Bed file with all the features from the annotation file "nb_allFeatures.gff3".
nb_allFeatures_renamepath_annotate.gff3 Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 92.5 MB - MD5: f9a87d3c48157c180a641b65d0d89412 Data Annotation file of the genome Nipponbare adapted from the Rice Genome Annotation Project, available at https://rice.uga.edu/.
O127_H6_E2348_69_193637c.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 4.8 MB - MD5: ad214c5247cba57dc04534a108ef3a92 Data Fasta file of the genome O127_H6_E2348_69_193637c, from the paper available at http://dx.doi.org/10.7554/eLife.78834.
readme_data.txt Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 5.7 KB - MD5: 8394446a4ae71c7c0b3b8709b665f196 Documentation Contains a description of all files in this dataset.
refpath_odgi Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 663 B - MD5: 52f6a241090f7c84ec4bb2647a25c280 Text file necessary to run ODGI on the rice data.
refpath_vg Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 687 B - MD5: f46438fd1982895d067497b239b317c5 Data Text file necessary to run VG on the rice data.
sequence_filter_rename_K_12_MG1655_09949b0.gff3 Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 2.6 MB - MD5: 98cd96703f495ba1a8ae4c35377c3b78 Data Annotation file of the genome K_12_MG1655_09949b0, adapted from https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 to match the pangenome graph.
AzucenaRS1.gff Mar 10, 2025 - Output from the analysis described in GrAnnoT paper Unknown - 115.0 MB - MD5: 8ec501c64ac6efea462461e07c7cb267 Data Result of GrAnnoT annotation transfer from Nipponbare (IRGSP).
AzucenaRS1.gff Mar 10, 2025 - Output from the analysis described in GrAnnoT paper Unknown - 115.0 MB - MD5: 01f29a93b8ae3ed9ebfcbfd5589f46b2 Data Result of the first transfer by GrAnnoT for the back and forth comparison with Liftoff.
AzucenaRS1.gff3 Mar 10, 2025 - Output from the analysis described in GrAnnoT paper Unknown - 98.9 MB - MD5: eaa7a2f213413765c781bb859eea2a5d Data Result of the first transfer by Liftoff for the back and forth comparison with GrAnnoT.

nb_allFeatures_renamed_filter.bed

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

PLINK Binary - 92.5 MB -

Data

Bed file with all the features from the annotation file "nb_allFeatures.gff3".

nb_allFeatures_renamepath_annotate.gff3

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 92.5 MB -

Data

Annotation file of the genome Nipponbare adapted from the Rice Genome Annotation Project, available at https://rice.uga.edu/.

O127_H6_E2348_69_193637c.fasta

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 4.8 MB -

Data

Fasta file of the genome O127_H6_E2348_69_193637c, from the paper available at http://dx.doi.org/10.7554/eLife.78834.

readme_data.txt

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 5.7 KB -

Documentation

Contains a description of all files in this dataset.

refpath_odgi

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 663 B -

Text file necessary to run ODGI on the rice data.

refpath_vg

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 687 B -

Data

Text file necessary to run VG on the rice data.

sequence_filter_rename_K_12_MG1655_09949b0.gff3

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 2.6 MB -

Data

Annotation file of the genome K_12_MG1655_09949b0, adapted from https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 to match the pangenome graph.

AzucenaRS1.gff

Mar 10, 2025 - Output from the analysis described in GrAnnoT paper

Unknown - 115.0 MB -

Data

Result of GrAnnoT annotation transfer from Nipponbare (IRGSP).

AzucenaRS1.gff

Mar 10, 2025 - Output from the analysis described in GrAnnoT paper

Unknown - 115.0 MB -

Data

Result of the first transfer by GrAnnoT for the back and forth comparison with Liftoff.

AzucenaRS1.gff3

Mar 10, 2025 - Output from the analysis described in GrAnnoT paper

Unknown - 98.9 MB -

Data

Result of the first transfer by Liftoff for the back and forth comparison with GrAnnoT.

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