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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.

2021-03-12 bioinformatics
10.1101/2021.03.11.434800 bioRxiv
Show 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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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.