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Galaxy Series: Data Intensive and Reproducible Research

Launched at the 2013 Galaxy Community Conference, this thematic series of articles highlighting papers relating to the Galaxy platform for computational research in the life and biomedical sciences. Focusing on toolkits, applications and best practice, articles can also take advantage of the GigaScience GigaGalaxy server to archive and host histories, analyses and tools to promote reproducible and transparent research.

  1. Content type: Technical Note

    Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potent...

    Authors: Robert L. Davidson, Ralf J. M. Weber, Haoyu Liu, Archana Sharma-Oates and Mark R. Viant

    Citation: GigaScience 2016 5:10

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  2. Content type: TECHNICAL NOTE

    With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing...

    Authors: Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru and Pierre Peterlongo

    Citation: GigaScience 2016 5:9

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  3. Content type: Technical Note

    The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale p...

    Authors: Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson and Nicola Soranzo

    Citation: GigaScience 2015 4:39

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  4. Content type: Technical Note

    Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data through its web interface. However, the process of adding ...

    Authors: Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai and Olivier Collin

    Citation: GigaScience 2015 4:22

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  5. Content type: Technical Note

    Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. However, since most bioinformatics tools are developed for comm...

    Authors: Yinan Wan, Daniel W Renner, Istvan Albert and Moriah L Szpara

    Citation: GigaScience 2015 4:19

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  6. Content type: Technical Note

    Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view...

    Authors: Saskia Hiltemann, Youri Hoogstrate, Peter van der Spek, Guido Jenster and Andrew Stubbs

    Citation: GigaScience 2014 3:19

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  7. Content type: Technical Note

    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, ...

    Authors: Saskia Hiltemann, Hailiang Mei, Mattias de Hollander, Ivo Palli, Peter van der Spek, Guido Jenster and Andrew Stubbs

    Citation: GigaScience 2014 3:1

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  8. Content type: Research

    Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for...

    Authors: Oscar C Bedoya-Reina, Aakrosh Ratan, Richard Burhans, Hie Lim Kim, Belinda Giardine, Cathy Riemer, Qunhua Li, Thomas L Olson, Thomas P Loughran Jr, Bridgett M vonHoldt, George H Perry, Stephan C Schuster and Webb Miller

    Citation: GigaScience 2013 2:17

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