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Publication Year: 2025

1,031 to 1,040 of 1,327 Results

AzucenaRS1.fna Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 368.4 MB - MD5: d621f8e18ef4fce7aef9ddb0b00db2cf Data Fasta file of the genome AzucenaRS1, 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).
IRGSP_nipponbare.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 363.7 MB - MD5: e923ca38bac7f347ffbf88142b93428f Fasta file of the genome Nipponbare, from the paper from 2013 by Kawahara, Y., de la Bastide, M., Hamilton, J.P. et al., "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data" (doi:10.1186/1939-8433-6-4).
IRGSP_nipponbare.genome Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 539 B - MD5: 562caffe11637996021726b3d3a2e59b Data Text file necessary to run VG on the rice data.
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.
nb_allFeatures.fa Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 626.5 MB - MD5: 25854fb0391bc1676dcddc967fdf3371 Data Fasta file of all the features from the annotation file "nb_allFeatures.gff3".
nb_allFeatures.gff3 Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 77.7 MB - MD5: 4a8e0be436e73bdf85baa362947c6dba Data Annotation file of the genome Nipponbare from the Rice Genome Annotation Project, available at https://rice.uga.edu/.
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/.
liftoff_transfer_chm13_to_grch38.gff Mar 10, 2025 - Output from the analysis described in GrAnnoT paper Unknown - 160.9 MB - MD5: a944747959786332e338b42bce913de8 Data Result of the human Chr1 annotation transfer by Liftoff

AzucenaRS1.fna

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

Unknown - 368.4 MB -

Data

Fasta file of the genome AzucenaRS1, 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).

IRGSP_nipponbare.fasta

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

Unknown - 363.7 MB -

Fasta file of the genome Nipponbare, from the paper from 2013 by Kawahara, Y., de la Bastide, M., Hamilton, J.P. et al., "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data" (doi:10.1186/1939-8433-6-4).

IRGSP_nipponbare.genome

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

Unknown - 539 B -

Data

Text file necessary to run VG on the rice data.

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.

nb_allFeatures.fa

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

Unknown - 626.5 MB -

Data

Fasta file of all the features from the annotation file "nb_allFeatures.gff3".

nb_allFeatures.gff3

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

Unknown - 77.7 MB -

Data

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

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/.

liftoff_transfer_chm13_to_grch38.gff

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

Unknown - 160.9 MB -

Data

Result of the human Chr1 annotation transfer by Liftoff

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