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Datasets

Dataset1 - 18 human genomes

Dataset ID Assembly Accession Assembly Name Download Link
1 GCA_009914755.4 CHM13_T2T_v2.0 https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz
2 GCA_000001405.28 GRCh38.p13 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GCA_000001405.28_GRCh38.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
3 GCA_011064465.1 Ash1.7 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/011/064/465/GCA_011064465.1_Ash1.7/GCA_011064465.1_Ash1.7_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
4 GCA_002180035.3 HG00514_prelim_3.0 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/180/035/GCA_002180035.3_HG00514_prelim_3.0/GCA_002180035.3_HG00514_prelim_3.0_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
5 GCA_001524155.4 NA19240_prelim_3.0 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/524/155/GCA_001524155.4_NA19240_prelim_3.0/GCA_001524155.4_NA19240_prelim_3.0_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
6 GCA_003634875.1 HG00733_Phased_Diploid_phase0 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/634/875/GCA_003634875.1_HG00733_Phased_Diploid/GCA_003634875.1_HG00733_Phased_Diploid_assembly_structure/phase0/assembled_chromosomes/FASTA/
7 GCA_014905855.1 ASM1490585v1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/905/855/GCA_014905855.1_ASM1490585v1/GCA_014905855.1_ASM1490585v1_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
8 GCA_002077035.3 NA12878_prelim_3.0 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/077/035/GCA_002077035.3_NA12878_prelim_3.0/GCA_002077035.3_NA12878_prelim_3.0_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
9 GCA_016700455.2 mHomSap3.pat https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/700/455/GCA_016700455.2_mHomSap3.pat/GCA_016700455.2_mHomSap3.pat_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
10 GCA_016695395.2 mHomSap3.mat https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/695/395/GCA_016695395.2_mHomSap3.mat/GCA_016695395.2_mHomSap3.mat_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
11 GCA_015476435.1 HC1-N https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/015/476/435/GCA_015476435.1_HC1-N/GCA_015476435.1_HC1-N_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
12 GCA_001292825.2 HS1011_v1.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/292/825/GCA_001292825.2_HS1011_v1.1/GCA_001292825.2_HS1011_v1.1_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
13 GCA_000306695.2 CHM1_1.1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/306/695/GCA_000306695.2_CHM1_1.1/GCA_000306695.2_CHM1_1.1_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
14 GCA_000002125.2 HuRef https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/125/GCA_000002125.2_HuRef/GCA_000002125.2_HuRef_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
15 GCA_000212995.1 HuRefPrime https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/212/995/GCA_000212995.1_HuRefPrime/GCA_000212995.1_HuRefPrime_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
16 GCA_003634875.1 HG00733_Phased_Diploid_phase1 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/634/875/GCA_003634875.1_HG00733_Phased_Diploid/GCA_003634875.1_HG00733_Phased_Diploid_assembly_structure/phase1/assembled_chromosomes/FASTA/
17 GCA_001712695.1 KOREF1.0 https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/712/695/GCA_001712695.1_KOREF1.0/GCA_001712695.1_KOREF1.0_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
18 GCA_000002115.2 WGSA https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/115/GCA_000002115.2_WGSA/GCA_000002115.2_WGSA_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/

Dataset2 - small genome datasets

Dataset Name Number of Sequences Mean Length without N Mean Length with N Data size/MB Download Link
Mitochondrial-genome 672 16,568 16,568 10.6 http://lab.malab.cn/soft/halign/data/mt1x.zip
Neisseria-meningitidis 5 2,190,088 2,190,088 10.4 https://github.com/malabz/Halign-G-data/raw/main/data/Neisseria-meningitidis.zip
Streptococcus-pneumoniae 11 2,138,975 2,139,054 22.4 https://github.com/malabz/Halign-G-data/raw/main/data/Streptococcus-pneumoniae.zip
Escherichia-coil 30 5,060,511 5,060,749 144.8 https://github.com/malabz/Halign-G-data/raw/main/data/Escherichia-coil.zip.001
https://github.com/malabz/Halign-G-data/raw/main/data/Escherichia-coil.zip.002
3Human-chromosome-1 3 231,424,778 231,424,778 662.1 https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.001
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.002
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.003
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.004
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.005
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.006
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.007
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.008
https://github.com/malabz/Halign-G-data/raw/main/data/3-Human-chromosome-1.zip.009