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Published on: February 18, 2022
Refget: standardized access to reference sequences
Andrew D Yates1,2, Jeremy Adams2,3, Somesh Chaturvedi1,4
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Motivation:
Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing.
Results:
We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations.
Availability And Implementation:
The refget specification can be found at: https://w3id.org/ga4gh/refget.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
