A human reference genome defines the coordinate system used to map sequencing reads and report variants. Multiple builds exist, and sequencing, variant, and annotation files must use compatible versions to ensure correct interpretation.
Human reference genome assemblies in practice
| Assembly | Release year | UCSC name | Status | Recommended use |
|---|---|---|---|---|
| GRCh38 | 2013 | hg38 | Current standard | Default for new work |
| T2T-CHM13 | 2022 | hs1 | Emerging | Research and future pipelines |
| GRCh37 | 2009 | hg19 | Legacy | Legacy datasets |
| Human Pangenome Reference | 2023– | — | Emerging | Population references |
| Build 36 | 2006 | hg18 | Historical | Old archives only |
| Build 35 | 2004 | hg17 | Historical | Rare legacy |
| GRCh39 | — | — | Postponed | Not available |
Chromosomes ideogram of the human reference genome assembly GRCh38/hg38. Public domain source: Wikimedia Commons.
Assembly naming differences
Reference assemblies are released by the Genome Reference Consortium (GRC) and NCBI under names such as GRCh37 and GRCh38. The UCSC Genome Browser distributes the same assemblies under identifiers such as hg19 and hg38.
These usually refer to the same coordinate system, but chromosome naming conventions may differ, for example chr1 in UCSC versus 1 in Ensembl or NCBI. Files must use consistent naming to remain compatible.
The sections below provide operational details for each assembly.
GRCh38
Release year: 2013
UCSC browser name: hg38
NCBI assembly accession: GCA_000001405.29
Status: Current global standard
Use in practice: Default reference for new clinical and research pipelines. Coordinates remain compatible across patch releases such as GRCh38.p14 (2022), which improve sequence representation without changing positions.
Official homepage:
https://www.ncbi.nlm.nih.gov/grc/human
T2T-CHM13
Release year: 2022
UCSC browser name: hs1
NCBI assembly accession: GCA_009914755.4
Status: Emerging reference
Use in practice: First gapless human genome assembly, enabling analysis of centromeres and previously unresolved regions. Increasingly used in research and method development, but not yet the standard coordinate system in clinical pipelines.
Official homepage:
https://github.com/marbl/CHM13
GRCh37
Release year: 2009
UCSC browser name: hg19
NCBI assembly accession: GCA_000001405.14
Status: Legacy standard
Use in practice: Still widely encountered in historical sequencing studies and clinical archives. Many variant databases and pipelines still use GRCh37, requiring compatibility when analysing legacy data.
Official homepage:
https://www.ncbi.nlm.nih.gov/grc/human
Human Pangenome Reference
Initial releases: 2023 onward
UCSC browser name: none
NCBI accession: multiple assemblies
Status: Emerging paradigm
Use in practice: Represents genomic diversity using multiple complete assemblies and graph-based approaches. Improves variant discovery in diverse populations but does not yet replace linear references in standard production pipelines.
Official homepage:
https://humanpangenome.org
Build 36 (hg18)
Release year: 2006
UCSC browser name: hg18
Status: Historical
Use in practice: Appears in early GWAS and archived sequencing projects. Rarely used in modern analysis but still encountered in historical datasets.
Reference portal:
https://genome.ucsc.edu
Build 35 (hg17)
Release year: 2004
UCSC browser name: hg17
Status: Historical
Use in practice: Very rare in current workflows but may appear in older archives or early sequencing studies.
Reference portal:
https://genome.ucsc.edu
GRCh39 (planned)
Status: Release postponed indefinitely
Use in practice: No official assembly available. Included here only to prevent confusion when future releases are discussed.
Official homepage:
https://www.ncbi.nlm.nih.gov/grc/human
How to interpret assembly naming
Assembly versus annotation
Assemblies define coordinates. Annotation releases such as Ensembl or GENCODE are layered onto assemblies and update independently.
Patch releases
Versions such as GRCh38.p14 update sequence representation without changing coordinates.
Linear references versus pangenome
GRCh37 and GRCh38 use a single linear genome. Pangenome resources use multiple genomes or graph representations and are not yet universal replacements.
Naming differences
Chromosomes may be labelled differently across tools, for example chr1 versus 1. Files must use consistent naming.
Practical usage guidance
New pipelines
Use GRCh38 unless compatibility with legacy datasets requires GRCh37.
Legacy datasets
Analyse data in the original assembly when possible. Migration typically requires coordinate conversion or remapping.
Archival storage
Alignment files should retain reference assembly information to allow correct reuse.
Migration considerations
Variant data can often be lifted between builds. Aligned read data typically require remapping for consistency.
Common pitfalls avoided by this reference
• Mixing hg19 and b37 builds
• Treating patch releases as new assemblies
• Renaming contigs instead of remapping
• Assuming pangenome replaces GRCh38
• Ignoring coordinate compatibility
Official ecosystem resources
Genome Reference Consortium
https://www.ncbi.nlm.nih.gov/grc/human
NCBI Assembly database
https://www.ncbi.nlm.nih.gov/assembly
UCSC Genome Browser
https://genome.ucsc.edu
Ensembl Genome Browser
https://www.ensembl.org
T2T Consortium
https://github.com/marbl/CHM13
Human Pangenome Reference Consortium
https://humanpangenome.org
This page is designed as a stable operational reference and can be updated as new assemblies or ecosystem standards emerge.
