Expanding the Galaxy's reference data

Nagampalli Vijaykrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Marius Van Den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michał Stolarczyk, Nathan C. Sheffield, Simon Gladman, Gianmauro Cuccuru, Björn Grüning, Nicola Soranzo, Helena Rasche, Bradley W. Langhorst, Matthias Bernt, Dan Fornika, David Anderson De Lima MoraisMichel Barrette, Peter Van Heusden, Mauro Petrillo, Antonio Puertas-Gallardo, Alex Patak, Hans Rudolf Hotz, Daniel Blankenberg*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.

Original languageEnglish
Article numbervbac030
JournalBioinformatics Advances
Volume2
Issue number1
DOIs
Publication statusPublished - 29 Apr 2022

Bibliographical note

Funding
This work was supported by funds provided by the Cleveland Clinic; the National Institutes of Health [U24HG006620, U24CA231877]; the Biotechnology and Biological Sciences Research Council, part of UK Research and Innovation [BB/CCG1720/1 to N.S., BBS/E/T/000PR9814 to N.S.]; the Novartis Research Foundation [to H.-R.H.]; the South African Research
Chairs Initiatives of the Department of Science and Technology and National Research Foundation of South Africa [64751 to P.V.H.]; the Research Foundation—Flanders [I002819N]; and the European Union’s Horizon 2020 programme [824087].

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press.

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