Published October 8, 2025 | Version data_v0.2.32
Software Open

SACGF/cdot: data_v0.2.32

Creators

  • 1. Centre for Cancer Biology ACRF Cancer Genomics facility
  • 2. CUBI Core Unit Bioinformatics, Berlin Institute of Health

Description

cdot-0.2.32.ensembl.GRCh37.json.gz

Method: Merge historical Urls:

  • https://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz: 196501

cdot-0.2.32.Homo_sapiens_GRCh37_Ensembl_87.gtf.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz: 196501

cdot-0.2.32.ensembl.GRCh38.json.gz

Method: Merge historical Urls:

  • https://ftp.ensembl.org/pub/release-115/gtf/homo_sapiens/Homo_sapiens.GRCh38.115.gtf.gz: 509650
  • https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz: 15424
  • https://ftp.ensembl.org/pub/release-95/gtf/homo_sapiens/Homo_sapiens.GRCh38.95.gtf.gz: 11320
  • https://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz: 5036
  • https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz: 4367
  • https://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz: 4226
  • https://ftp.ensembl.org/pub/release-96/gtf/homo_sapiens/Homo_sapiens.GRCh38.96.gtf.gz: 3535
  • https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz: 2499
  • https://ftp.ensembl.org/pub/release-100/gtf/homo_sapiens/Homo_sapiens.GRCh38.100.gtf.gz: 1862
  • https://ftp.ensembl.org/pub/release-103/gtf/homo_sapiens/Homo_sapiens.GRCh38.103.gtf.gz: 1832
  • https://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/Homo_sapiens.GRCh38.101.gtf.gz: 1830
  • https://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz: 1803
  • https://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/Homo_sapiens.GRCh38.102.gtf.gz: 1462
  • https://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz: 1435
  • https://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz: 1077
  • https://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz: 947
  • https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/Homo_sapiens.GRCh38.109.gtf.gz: 907
  • https://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz: 861
  • https://ftp.ensembl.org/pub/release-82/gtf/homo_sapiens/Homo_sapiens.GRCh38.82.gtf.gz: 793
  • https://ftp.ensembl.org/pub/release-105/gtf/homo_sapiens/Homo_sapiens.GRCh38.105.gtf.gz: 708
  • https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.gtf.gz: 633
  • https://ftp.ensembl.org/pub/release-114/gtf/homo_sapiens/Homo_sapiens.GRCh38.114.gtf.gz: 602
  • https://ftp.ensembl.org/pub/release-107/gtf/homo_sapiens/Homo_sapiens.GRCh38.107.gtf.gz: 526
  • https://ftp.ensembl.org/pub/release-89/gtf/homo_sapiens/Homo_sapiens.GRCh38.89.gtf.gz: 384
  • https://ftp.ensembl.org/pub/release-108/gtf/homo_sapiens/Homo_sapiens.GRCh38.108.gtf.gz: 337
  • https://ftp.ensembl.org/pub/release-113/gtf/homo_sapiens/Homo_sapiens.GRCh38.113.gtf.gz: 268
  • https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz: 260

cdot-0.2.32.Homo_sapiens_GRCh38_Ensembl_112.gtf.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz: 254129

cdot-0.2.32.Homo_sapiens_GRCh38_Ensembl_113.gtf.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ensembl.org/pub/release-113/gtf/homo_sapiens/Homo_sapiens.GRCh38.113.gtf.gz: 387944

cdot-0.2.32.Homo_sapiens_GRCh38_Ensembl_114.gtf.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ensembl.org/pub/release-114/gtf/homo_sapiens/Homo_sapiens.GRCh38.114.gtf.gz: 387954

cdot-0.2.32.Homo_sapiens_GRCh38_Ensembl_115.gtf.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ensembl.org/pub/release-115/gtf/homo_sapiens/Homo_sapiens.GRCh38.115.gtf.gz: 509650

cdot-0.2.32.ensembl.T2T-CHM13v2.0.json.gz

Method: Merge historical Urls:

  • https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/geneset/2022_07/Homo_sapiens-GCA_009914755.4-2022_07-genes.gtf.gz: 236651
  • https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/geneset/2022_06/Homo_sapiens-GCA_009914755.4-2022_06-genes.gtf.gz: 1838

cdot-0.2.32.all-builds-refseq-grch37_grch38_t2t-chm13v2.0.json.gz

Method: Combine multiple genome builds Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2025_08/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 180091
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2025_08/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 178096
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.25-RS_2024_09/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 89909
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20211119/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 75738
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.107/GFF/ref_GRCh38.p2_top_level.gff3.gz: 72137
  • postgresql://uta.biocommons.org/uta_20241220: 47669
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.108/GFF/ref_GRCh38.p7_top_level.gff3.gz: 45908
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gff.gz: 38043
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz: 37273
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.106/GFF/ref_GRCh38_top_level.gff3.gz: 34396
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20190906/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 15490
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20200522/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 12841
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/BUILD.37.3/GFF/ref_GRCh37.p5_top_level.gff3.gz: 3978
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20190607/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 3876
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 3637
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2023_03/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 2374
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2023_03/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 2176
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20210514/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 2131
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20201022/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 1948
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20190905/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1943
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2024_08/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 1923
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2024_08/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 1912
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 1817
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.104/GFF/ref_GRCh37.p10_top_level.gff3.gz: 1757
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20200815/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1667
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20200228/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1645
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20191205/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1581
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20210226/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1425
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20201120/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 939
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.103/GFF/ref_GRCh37.p9_top_level.gff3.gz: 534
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20220307/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 462
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2023_10/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 450
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2023_10/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 413

cdot-0.2.32.refseq.GRCh37.json.gz

Method: Merge historical Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.25-RS_2024_09/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 90364
  • postgresql://uta.biocommons.org/uta_20241220: 45969
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz: 37307
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20190906/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 15504
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/BUILD.37.3/GFF/ref_GRCh37.p5_top_level.gff3.gz: 3980
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20201022/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 1961
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.104/GFF/ref_GRCh37.p10_top_level.gff3.gz: 1757
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.103/GFF/ref_GRCh37.p9_top_level.gff3.gz: 534
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20220307/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 470

cdot-0.2.32.Homo_sapiens_GRCh37_RefSeq_105.20201022.gff.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20201022/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 78617

cdot-0.2.32.Homo_sapiens_GRCh37_RefSeq_105.20220307.gff.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/105.20220307/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz: 82466

cdot-0.2.32.refseq.GRCh38.json.gz

Method: Merge historical Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2025_08/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 178369
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20211119/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 75738
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.107/GFF/ref_GRCh38.p2_top_level.gff3.gz: 72137
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.108/GFF/ref_GRCh38.p7_top_level.gff3.gz: 45908
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gff.gz: 38043
  • https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.106/GFF/ref_GRCh38_top_level.gff3.gz: 34396
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20200522/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 12841
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20190607/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 3876
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 3641
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2023_03/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 2178
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20210514/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 2131
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20190905/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1943
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2024_08/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 1927
  • postgresql://uta.biocommons.org/uta_20241220: 1720
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20200815/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1667
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20200228/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1645
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20191205/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1581
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20210226/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 1425
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/109.20201120/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz: 939
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2023_10/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 414

cdot-0.2.32.Homo_sapiens_GRCh38_RefSeq_110.gff.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 175146

cdot-0.2.32.Homo_sapiens_GRCh38_RefSeq_RS_2025_08.gff.json.gz

Method: Single GFF3 file Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_000001405.40-RS_2025_08/GCF_000001405.40_GRCh38.p14_genomic.gff.gz: 178369

cdot-0.2.32.refseq.T2T-CHM13v2.0.json.gz

Method: Merge historical Urls:

  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2025_08/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 180091
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2023_03/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 2374
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2024_08/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 1912
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 1817
  • https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/GCF_009914755.1-RS_2023_10/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz: 450

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Additional details

Related works

Is supplement to
Software: https://github.com/SACGF/cdot/tree/data_v0.2.32 (URL)

Software

Repository URL
https://github.com/SACGF/cdot