Refget: standardised access to reference sequences

Yates, A. D.; Adams, J.; Chaturvedi, S.; Davies, R. M.; Laird, M.; Leinonen, R.; Nag, R.; Sheffield, N. C.; Hofmann, O.; Keane, T.

doi:10.1101/2021.03.11.434800

bioRxiv · 10.1101/2021.03.11.434800

Refget: standardised access to reference sequences

Yates, A. D.·Adams, J.·Chaturvedi, S.·Davies, R. M.·Laird, M.·Leinonen, R.·Nag, R.·Sheffield, N. C.·Hofmann, O.·Keane, T.

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Abstract

Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. 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. https://w3id.org/ga4gh/refget.

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Yates, A. D., Adams, J., Chaturvedi, S., Davies, R. M., Laird, M., Leinonen, R., Nag, R., Sheffield, N. C., Hofmann, O., Keane, T.. 2021-03-12. Refget: standardised access to reference sequences. https://doi.org/10.1101/2021.03.11.434800

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