TY - JOUR
T1 - Expanding the Galaxy's reference data
AU - Vijaykrishna, Nagampalli
AU - Joshi, Jayadev
AU - Coraor, Nate
AU - Hillman-Jackson, Jennifer
AU - Bouvier, Dave
AU - Van Den Beek, Marius
AU - Eguinoa, Ignacio
AU - Coppens, Frederik
AU - Davis, John
AU - Stolarczyk, Michał
AU - Sheffield, Nathan C.
AU - Gladman, Simon
AU - Cuccuru, Gianmauro
AU - Grüning, Björn
AU - Soranzo, Nicola
AU - Rasche, Helena
AU - Langhorst, Bradley W.
AU - Bernt, Matthias
AU - Fornika, Dan
AU - De Lima Morais, David Anderson
AU - Barrette, Michel
AU - Van Heusden, Peter
AU - Petrillo, Mauro
AU - Puertas-Gallardo, Antonio
AU - Patak, Alex
AU - Hotz, Hans Rudolf
AU - Blankenberg, Daniel
N1 - Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
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U2 - 10.1093/bioadv/vbac030
DO - 10.1093/bioadv/vbac030
M3 - Article
C2 - 35669346
AN - SCOPUS:85148568863
SN - 2635-0041
VL - 2
JO - Bioinformatics Advances
JF - Bioinformatics Advances
IS - 1
M1 - vbac030
ER -