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Publication Year: 2025

1,021 to 1,030 of 1,316 Results

EcoliGraph_MGC.gfa Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 112.8 MB - MD5: e5183acfb527fcd7b01ac4386d7be290 Data E.coli pangenome graph built with 12 genomes from the paper available at http://dx.doi.org/10.7554/eLife.78834.
chm13.draft_v1.1_chr1.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 240.8 MB - MD5: ab2421da8b88a867d087c3f452a6969f Fasta file of the chromosome 1 of the genome CHM13,from https://projects.ensembl.org/hprc/.
CHM13_chr1.gff Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 152.4 MB - MD5: 1f0269e5728a0ed5f83188cd08792c41 Data Annotation file of the chromosome 1 of the genome CHM13, adapted from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ to match the pangenome graph.
feature_types.txt Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 638 B - MD5: 571dcfb312543edd81dca0524212459a Lists all the feature types in the human annotation (CHM13_chr1.gff), necessary to run Liftoff on all the features.
GCA_000001405.15_GRCh38_chr1.fna Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 240.8 MB - MD5: 90780be24a8555613e6ad0bd2f8a0935 Data Fasta file of the chromosome 1 of the genome GRCh38,from https://projects.ensembl.org/hprc/.
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.

EcoliGraph_MGC.gfa

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

Unknown - 112.8 MB -

Data

E.coli pangenome graph built with 12 genomes from the paper available at http://dx.doi.org/10.7554/eLife.78834.

chm13.draft_v1.1_chr1.fasta

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

Unknown - 240.8 MB -

Fasta file of the chromosome 1 of the genome CHM13,from https://projects.ensembl.org/hprc/.

CHM13_chr1.gff

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

Unknown - 152.4 MB -

Data

Annotation file of the chromosome 1 of the genome CHM13, adapted from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/ to match the pangenome graph.

feature_types.txt

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

Plain Text - 638 B -

Lists all the feature types in the human annotation (CHM13_chr1.gff), necessary to run Liftoff on all the features.

GCA_000001405.15_GRCh38_chr1.fna

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

Unknown - 240.8 MB -

Data

Fasta file of the chromosome 1 of the genome GRCh38,from https://projects.ensembl.org/hprc/.

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.

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