referenssigenomin

Referenssigenomin is a term used in genomics to describe a standardized naming and citation framework for reference genomes and their assemblies. Although not widely codified as an official term, it serves as a useful concept for discussing how reference genomes are identified, named, and versioned across databases and literature. Although not widely codified as an official term, it serves as a useful concept for discussing how reference genomes are identified, named, and versioned across databases and literature.

Its etymology draws on referens (reference) and genom (genome) to emphasize standardization. The concept covers the assignment of stable names, the use of database accessions, and the recording of assembly versions that enable precise comparison across studies.

Its primary purpose is to promote reproducibility and interoperability. By clearly specifying the reference genome used, researchers and software can reproduce analyses and coordinate results across platforms and publications.

Key components of referenssigenomin include: assembly name (such as GRCh38 or GRCm38), species and taxonomy, version or patch level (for example p13), and whether the assembly is the primary reference or includes alternate haplotypes or decoy sequences. It also involves assembly accessions (e.g., GCA_000001405.28) that uniquely identify the exact data set.

Examples commonly cited under this framework are the human reference GRCh38.p13 and the mouse reference GRCm38.p6. In practice, researchers must note the exact assembly name and accession to avoid misalignment of coordinates when upgrading to newer references.

Relation to existing standards includes alignment with RefSeq and ENSEMBL nomenclature, and adherence to INSDC accession practices. Challenges include coordinate liftover between assemblies and keeping up with frequent updates to reference genomes.