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Reference Sequences

NCBI mouse reference genome assemblies

We provide the NCBI mouse reference assembly used by the Sanger Mouse Genomics group for NCBIM37 and GRCm38. This is a reliable source where the appropriate contigs have already been selected by experts. NCBIM37 is annotated with Ensembl release 67 and GRCm38 with Ensembl release 68.

UCSC mouse reference genome assemblies

The assembly sequence is in one file per chromosome and is available for mm9 and mm10. We concatenated all the chromosome files to one final fasta file for each genome assembly.

NCBI human reference genome assemblies

  • GRCh37: We provide the version used by the 1000genomes project as it is widely used and recommended. The chromosomes and contigs are already concatenated.
    • g1k_phase1/hs37: This reference sequence contains the autosomal and both sex chromosomes, an updated mitochondrial chromosome as well as "non-chromosomal supercontigs". The README explains the method of construction.
    • g1k_phase2/hs37d5: In addition to these sequences the phase 2 reference sequence contains the herpes virus genome and decoy sequences for improving SNP calling.
  • GRCh38: The GRCh38 assembly offers an "analysis set" that was created to accommodate next generation sequencing read alignment pipelines. We provide the three analysis sets from the NCBI.
    • hs38/no_alt_analysis_set: The chromosomes, mitochondrial genome, unlocalized scaffolds, unplaced scaffolds and the Epstein-Barr virus sequence which has been added as a decoy to attract contamination in samples.
    • hs38a/full_analysis_set: the alternate locus scaffolds in addition to all the sequences present in the no_alt_analysis_set.
    • hs38DH/full_plus_hs38d1_analysis_set: contains the human decoy sequences from hs38d1 in addition to all the sequences present in the full_analysis set. More detailed information is available in the README.

UCSC human reference genome assemblies

The assembly sequence is in one file per chromosome is available for hg18, hg19 and hg38. We concatenated all the chromosome files to one final fasta file for each genome assembly. Additionally, in the subfolder chromosomes we keep the chromosome fasta files separately for hg18 and hg19.

Other reference genomes

  • danRer10: UCSC/GRC zebrafish build 10
  • dm6: UCSC/GRC Drosophila melanogaster build 6
  • ecoli:
    • GCA_000005845.2_ASM584v2: Genbank Escherichia coli K-12 subst. MG1655 genome
  • genomemedley:
    • 1: Concatenated genome of hg19, dm6, mm10; Chromosomes are tagged with corresponding organism
  • PhiX: Control genome that is used by Illumina for sequencing runs
  • sacCer3: UCSC's Saccharomyces cerevisiae genome build 3
  • UniVec:
    • 9: NCBI's non redundant reference of vector sequences, adapters, linkers and primers commonly used in the process of cloning cDNA or genomic DNA (build 9)
  • UniVec_Core
    • 9: A subset of UniVec build 9

The following directory structure indicates the available genomes. Where there isn't a name for the data set, either the source (e.g. sanger - from the Sanger Mouse Genomes project) or the download date is used to name the sub-directory.

static_data/reference
├── danRer10
│   └── ucsc
├── dm6
│   └── ucsc
├── ecoli
│   └── GCA_000005845.2_ASM584v2
├── genomemedley
│   └── 1
├── GRCh37
│   ├── g1k_phase1
│   ├── g1k_phase2
│   ├── hs37
│   └── hs37d5
├── GRCh38
│   ├── hs38
│   ├── hs38a
│   └── hs38DH
├── GRCm38
│   └── sanger
├── hg18
│   └── ucsc
├── hg19
│   └── ucsc
├── hg38
│   └── ucsc
├── mm10
│   └── ucsc
├── mm9
│   └── ucsc
├── NCBIM37
│   └── sanger
├── phix
│   └── illumina
├── sacCer3
│   └── ucsc
├── UniVec
│   └── 9
└── UniVec_Core
    └── 9

Last update: April 20, 2022