The Global Alliance for Genomics and Health (GA4GH) has announced the release of refget Sequence Collections, a newly approved product that simplifies the management and comparison of reference genome assemblies developed by researchers including those at EMBL’s European Bioinformatics Institute (EMBL-EBI) and the ELIXIR infrastructure. Refget Sequence Collections join the ranks of forty other products developed by members of GA4GH Work Streams to enable broad, responsible sharing of genomic and related health data. GA4GH products are designed to harness the power of global genomic data to foster improvements in human health outcomes.
“The refget Sequence Collections standard helps researchers easily confirm the exact assembly they are working with and helps to pinpoint and resolve discrepancies that could impact not only research but also clinical decisions down the line,” said Andy Yates, Team Leader at EMBL-EBI. “Ensuring absolute clarity about which reference sequences are being used can lead to more consistent, reproducible research and in a healthcare setting this translates into more accurate diagnostics and better patient outcomes.”
When researchers embark on a new genomic analysis, they often seek to compare their sequence data to a reference sequence. Reference sequences are commonly used to interpret biological data such as an individual’s genetic makeup.
Through this comparison, researchers can determine where genomic variations exist to better understand how these variations contribute to genetic diseases.
However, throughout the course of modern genomics, researchers have used different naming conventions for individual sequences, including a single chromosome or sequences of DNA, mRNA, and proteins. This means that identifying and locating the correct reference sequences can be challenging, making data integration and comparison a time-consuming manual process.
To address these challenges, GA4GH’s Large-Scale Genomics (LSG) Work Stream developed refget Sequences in 2018. The refget Sequences API uses an algorithm to assign a unique identifier – like a fingerprint – to a single sequence. An accompanying API allows researchers to do the reverse discovery as well, finding the original sequence from the name.
While the refget Sequences API provides a single name for a single reference sequence (for instance, a single chromosome), refget Sequence Collections assigns a name for a collection of reference sequences (for instance, a set of chromosomes, which makes up a genome or assembly).
“We don’t tend to work with single sequences,” said Timothee Cezard, Project Lead at EMBL-EBI. “We tend to work with groups of sequences which correspond to one genome.”
“The process of mapping data to coordinate systems derived from genome sequences is central to many workflows in fields such as epigenomics, transcriptomics, and biodiversity genomics,” said Sveinung Gundersen, Senior Engineer for ELIXIR Norway at the University of Oslo. “Refget Sequence Collections also aims to address long-standing issues related to assessing the compatibility of data files with genome browsers and other coordinate-based analysis tools.”
The next phase for the refget team is to incorporate refget Sequence Collections into widely used file format specifications; CRAM, BAM, SAM, and VCF. The team will also look to advance the standard further to develop algorithms that assign identifiers to human reference pangenomes — a collection of all the DNA sequences, or all of the genomes, in a group of individuals.
Read the full GA4GH press release for further details about refget Sequence Collections.
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