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Thread: Gambit - genome alignment viewer and analysis workbench

  1. #1
    Join Date
    Oct 2008
    Qt products
    MacOS X Unix/X11 Windows

    Default Gambit - genome alignment viewer and analysis workbench

    Hello fellow Qt hackers!

    Gambit is a visualization & analysis workbench for large genomic datasets, built using Qt.

    The beta release (v0.4.145) is available as of today (15 January 2010).
    If you work in bioinformatics or general genomic research, you might find this useful. Feel free to give it a test drive.

    All pre-compiled executables, documentation, source code, and test data are available on Google Code:

    Please post any bug reports, feature requests, etc to the Google Code "Issues" tracker.
    This is our first public beta release, so there are bound to be some minor and (hopefully few) major issues.
    Please let me know if anything seems broken, annoying, or awkward. I'll do my best to fix it.


    Here's a summary description:

    "Gambit is a new cross-platform GUI (graphical user interface) application for sequence visualization and analysis.

    Our software takes advantage of the indexing features of the (fairly) recently standardized BAM sequence alignment format that allows rapid access to genomic data, with minimal startup time and re-rendering delay. Gambit also supports a variety of annotation formats (BED, GFF, GFF3, VCF) “out-of-the-box” for displaying gene/region annotations as well as SNP entries.

    Gambit is currently “plugin-aware” with respect to format support, meaning support for new formats can be added without needing to modify/upgrade the main program itself.

    Bioinformatics analysis of sequence data currently requires specialized expertise and is rapidly becoming a bottleneck. Analysis needs of smaller biology laboratories can be served if the visualization software integrates essential analytical functionality. Such functionality includes PCR primer design to support candidate SNP validation experiments; connecting to common databases; exporting data from specific regions of the chromosome for detailed and focused analysis.

    Gambit will soon be “plugin-aware” with respect to analytical tools to provide such integrated functions. One benefit from implementing the analysis system via plugins is that anyone with programming skills can readily include their own custom features: support for new file formats, additional metrics, or even custom views. Another benefit is that users need not add every plugin. You will be able customize Gambit to be as lightweight or fully-functional as your needs require."


    Hopefully you guys will forgive my shameless borrowing from QtCreator style.

    I realize this may be out of the scope of interest for most users here. But if you do happen to give it a spin, I welcome any feedback either here or on the Google Code hosting site.

    Happy coding!

    // Derek
    Just Another Lowly Grad Student
    Marth Laboratory, Boston College
    Last edited by pezmaster31; 15th January 2010 at 22:51.

  2. #2
    Join Date
    Jun 2010
    Unix/X11 Windows

    Default Re: Gambit - genome alignment viewer and analysis workbench

    Hey pezmaster31,

    Gambit looks very promising! I do have a question though, something that my colleagues and I are (seemingly) always struggling with. Do you have any plans for including the ability to read next gen "out of the box" formats, like sff (maybe not, since this is pre-assembly) or quality files generated from 454 sequencing runs? It would be really handy to see what quality score each base was given from the assembly.

    Also: other file formats. How easy are they to integrate? Being able to natively imput alignments in (older, but still kind of standard) formats like FASTA, or ClustalW would be extremely handy.


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