Journal article
Refget: standardized access to reference sequences
AD Yates, J Adams, S Chaturvedi, RM Davies, M Laird, R Leinonen, R Nag, NC Sheffield, O Hofmann, TM Keane
Bioinformatics | OXFORD UNIV PRESS | Published : 2022
Open access
Abstract
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.
Grants
Awarded by European Commission
Funding Acknowledgements
This work was supported by the Wellcome Trust [grant numbers WT201535/Z/16/Z, 206194]; the Australian Genomics Health Alliance [NHMRC grant number 1113531]; the Australian Medical Research Future Fund; National Institute of General Medical Sciences under award number GM128636; and the European Molecular Biology Laboratory. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.