BACKGROUND: Complete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, requires annotation with various databases that often require command-line and/or programming experience; thus, limiting their use to the average research scientist. We have therefore implemented this CG toolkit, together with a number of annotation, visualisation and file manipulation tools in Galaxy called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy). FINDINGS: In order to provide research scientists with web-based, simple and accurate analytical and visualisation applications for the selection of candidate mutations from Complete Genomics data, we have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy. In addition we implemented some of the most popular command-line annotation and visualisation tools to allow research scientists to select candidate pathological mutations (SNV, and indels). Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules. CONCLUSIONS: CGtag provides a user-friendly interface to all research scientists wishing to select candidate variants from CG or other next-generation sequencing platforms' data. By using a cloud-based infrastructure, we can also assure sufficient and on-demand computation and storage resources to handle the analysis tasks. The tools are freely available for use from an NBIC/CTMM-TraIT (The Netherlands Bioinformatics Center/Center for Translational Molecular Medicine) cloud-based Galaxy instance, or can be installed to a local (production) Galaxy via the NBIC Galaxy tool shed.
BACKGROUND: Complete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, requires annotation with various databases that often require command-line and/or programming experience; thus, limiting their use to the average research scientist. We have therefore implemented this CG toolkit, together with a number of annotation, visualisation and file manipulation tools in Galaxy called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy). FINDINGS: In order to provide research scientists with web-based, simple and accurate analytical and visualisation applications for the selection of candidate mutations from Complete Genomics data, we have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy. In addition we implemented some of the most popular command-line annotation and visualisation tools to allow research scientists to select candidate pathological mutations (SNV, and indels). Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules. CONCLUSIONS:CGtag provides a user-friendly interface to all research scientists wishing to select candidate variants from CG or other next-generation sequencing platforms' data. By using a cloud-based infrastructure, we can also assure sufficient and on-demand computation and storage resources to handle the analysis tasks. The tools are freely available for use from an NBIC/CTMM-TraIT (The Netherlands Bioinformatics Center/Center for Translational Molecular Medicine) cloud-based Galaxy instance, or can be installed to a local (production) Galaxy via the NBIC Galaxy tool shed.
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Authors: Daniel Blankenberg; Gregory Von Kuster; Nathaniel Coraor; Guruprasad Ananda; Ross Lazarus; Mary Mangan; Anton Nekrutenko; James Taylor Journal: Curr Protoc Mol Biol Date: 2010-01
Authors: Joyce M G Florisson; Annemieke J M H Verkerk; Daphne Huigh; A Jeannette M Hoogeboom; Sigrid Swagemakers; Andreas Kremer; Daphne Heijsman; Maarten H Lequin; Irene M J Mathijssen; Peter J van der Spek Journal: Am J Med Genet A Date: 2013-08-15 Impact factor: 2.802
Authors: Andrew Stubbs; Elizabeth A McClellan; Sebastiaan Horsman; Saskia D Hiltemann; Ivo Palli; Stephan Nouwens; Anton Hj Koning; Frits Hoogland; Joke Reumers; Daphne Heijsman; Sigrid Swagemakers; Andreas Kremer; Jules Meijerink; Diether Lambrechts; Peter J van der Spek Journal: J Clin Bioinforma Date: 2012-11-19
Authors: Ioannis Karageorgos; Clint Mizzi; Efstathia Giannopoulou; Cristiana Pavlidis; Brock A Peters; Zoi Zagoriti; Peter D Stenson; Konstantinos Mitropoulos; Joseph Borg; Haralabos P Kalofonos; Radoje Drmanac; Andrew Stubbs; Peter van der Spek; David N Cooper; Theodora Katsila; George P Patrinos Journal: Hum Genomics Date: 2015-06-20 Impact factor: 4.639
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