G-OnRamp: A Galaxy-based platform for collaborative annotation of eukaryotic genomes

Yating Liu; Luke Sargent; Wilson Leung; Sarah C.R. Elgin; Jeremy Goecks

doi:10.1093/bioinformatics/btz309

G-OnRamp: A Galaxy-based platform for collaborative annotation of eukaryotic genomes

Yating Liu, Luke Sargent, Wilson Leung, Sarah C.R. Elgin, Jeremy Goecks

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

Summary: G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNASeq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings. Availability and implementation: The virtual machine images and tutorials are available on the G-OnRamp web site (http://g-onramp.org/deployments). The source code is available under an Academic Free License version 3.0 through the goeckslab GitHub repository (https://github.com/goeckslab).

Original language	English (US)
Pages (from-to)	4422-4423
Number of pages	2
Journal	Bioinformatics
Volume	35
Issue number	21
DOIs	https://doi.org/10.1093/bioinformatics/btz309
State	Published - Nov 1 2019

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btz309

Cite this

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title = "G-OnRamp: A Galaxy-based platform for collaborative annotation of eukaryotic genomes",

abstract = "Summary: G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNASeq data and repeat finders. G-OnRamp can be used to visualize large genomics datasets and to perform collaborative genome annotation projects in both research and educational settings. Availability and implementation: The virtual machine images and tutorials are available on the G-OnRamp web site (http://g-onramp.org/deployments). The source code is available under an Academic Free License version 3.0 through the goeckslab GitHub repository (https://github.com/goeckslab).",

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AU - Sargent, Luke

AU - Leung, Wilson

AU - Elgin, Sarah C.R.

AU - Goecks, Jeremy

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G-OnRamp: A Galaxy-based platform for collaborative annotation of eukaryotic genomes

Abstract

ASJC Scopus subject areas

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