NovaSeq X Series v1.4 Reference Genomes

Reference genomes for NovaSeq X Control Software v1.4.

Reference Genome Files for NovaSeq X Series v1.4
Name File Contents Download Link File Size Date
Human a la Carte Bundles chm13_v2-cnv.graph.hla.methyl_cg.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [T2T] CHM13_v2 v5 Pangenome 31.5 GB 5/13/2026
chm13_v2-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [T2T] CHM13_v2 v5 Genome 26.8 GB
hg38-alt_masked.cnv.graph.hla.methyl_cg.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [1000 Genomes] hg38 v5 Pangenome 30.2 GB
hg38-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [1000 Genomes] hg38 v5 Genome 24.9 GB
hg38-mm39-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [1000 Genomes] Mus Musculus [Gencode] - hg38-mm39 v5 Genome 28.2 GB
hs37d5_chr-cnv.graph.hla.methyl_cg.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [NCBI] hs37d5_chr v5 Pangenome 29.9 GB
hs37d5_chr-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [NCBI] hs37d5_chr v5 Genome 24.5 GB
hs37d5-cnv.graph.hla.methyl_cg.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [NCBI] hs37d5 v5 Pangenome 29.9 GB
hs37d5-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz Reference Genome: Homo sapiens [NCBI] hs37d5 v5 Genome 24.5 GB
mm10-methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz Reference Genome: Mus musculus [UCSC] mm10 v5 Genome 24.9 GB
Non-Human General Genome Bundle
  • A_Thaliana-rna-11-r5.0-2.tar.gz
  • Bacillus_cereus_ATCC_10987-cnv.rna-11-r5.0-2.tar.gz
  • eschColi_K12_1-cnv.rna-11-r5.0-2.tar.gz
  • lambda_phage-methyl_cg.methylated_combined-11-r5.0-2.tar.gz
  • Rhodobacter_sphaeroides_2.4.1_12905-cnv.rna.seed_len19-11-r5.0-2.tar.gz
  • WBcel235-rna-11-r5.0-2.tar.gz
  • Cereibacter_sphaeroides_ATCC_17023-rna-11-r5.0-2.tar.gz
  • Human_immunodeficiency_virus_1-rna-11-r5.0-2.tar.gz
  • Influenza_A_virus_H1N1-rna-11-r5.0-2.tar.gz
  • Influenza_A_virus_H3N2-rna-11-r5.0-2.tar.gz
  • Influenza_A_virus_H5N1-rna-11-r5.0-2.tar.gz
  • Mycobacterium_tuberculosis_H37Rv-rna-11-r5.0-2.tar.gz
  • phix-cnv.rna-11-r5.0-2.tar.gz
  • Saccharomyces_cerevisiae_S288C-rna-11-r5.0-2.tar.gz
  • Salmonella_enterica_LT2-rna-11-r5.0-2.tar.gz
  • SARS_coronavirus_2-rna-11-r5.0-2.tar.gz
  • Shigella_sonnei_SE6-1-rna-11-r5.0-2.tar.gz
  • Staphylococcus_aureus_NCTC_8325-rna-11-r5.0-2.tar.gz
  • Streptococcus_pneumoniae_Hu17-rna-11-r5.0-2.tar.gz
 Reference Genome: Non-Human General Genome Bundle 460 MB
Non-Human Mammal Genome Bundle
  • mm39-methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz
  • rn6-rna-11-r5.0-2.tar.gz
 Reference Genome: Non-Human Mammal Genome Bundle 32.1 GB
Reference Genome: Homo sapiens [UCSC] hg19 Alt Masked v5 Bundle
  • hg38-alt_masked.cnv.graph.hla.methyl_cg.rna-11-r5.0-2.tar.gz
  • hg38-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz
 Reference Genome: Homo sapiens [1000 Genomes] hg38 v5 Genome Bundle 54.5 GB
Reference Genome: Homo sapiens [1000 Genomes] hg38 v5 Graph Genome Bundle
  • hg38-alt_masked.cnv.graph.hla.methyl_cg.rna-11-r5.0-2.tar.gz
  • hg38-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-2.tar.gz
 Reference Genome: Homo sapiens [1000 Genomes] hg38 v5 Genome Bundle 55.1 GB
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