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Robert Kleta and His Newly-Formed Team Publish in a Few Short Months with SVS
Core Plus
SVS Core Plus offers a robust platform for efficiently managing, manipulating, and visualizing large genomic datasets, regardless of where the data came from or where analysis took place. Thus, even when using a separate command-line tool or other software program for analysis, SVS Core Plus can help eliminate many of the hassles of working with large data on the front-end and exploring it visually on the back-end.
Data Management
The core architecture of SVS has been designed to efficiently handle datasets of virtually any size and type on a desktop computer. SVS Core Plus natively supports over 70 different file formats and over 40 export formats to streamline data management, ensuring you spend most of your time on the more important aspects of analysis.
Data Editing and Manipulation
Real-time spreadsheet manipulation, data editing, and enrichment help eliminate the hassles of working with large-scale, complex data. Easily combine multiple sample sets and data of different types, from different arrays, or even platforms. Quickly recode genotypes based on a specified genetic model, flip DNA strands, transcode from AB to AGCT formats and more. Further, an integrated spreadsheet editor facilitates data editing and transformations on a grand scale.
Richly Interactive Data Visualization
SVS Core Plus comes with Golden Helix’s dynamic genome browser. View results from a whole new perspective with richly interactive visualization and unprecedented whole-genome navigation. Apply data transformations in real-time, or customize plots for more enhanced presentation. You can combine multiple data series from multiple populations to view graphs side-by-side. Annotation tracks add depth and understanding to your analysis. After you attain the desired view, you can easily save it to a number of publication quality formats, including scalable vector graphics.
Genomic Build, Marker Map, and Annotation Management
SVS Core Plus provides a robust set of tools for working with and managing genomic information. Easily switch among a wide-variety of supported species and genomic builds and apply genetic marker maps to ensure all analyses and visualizations are accurate based on correct genomic coordinates. Further, genomic annotations can be used to enrich analyses, provide meaning to results, or visualized alongside data for greater context in the genome browser. SVS provides real-time network access to an expanding list of genomic annotations. You can also use your own custom annotations from private sources or public databases, such as UCSC, RefSeq, and Ensemble.
Python Scripting
Python is a clear and powerful object-oriented programming language, comparable to Perl, Ruby, Scheme, or Java. SVS Core Plus gives you fully programmatic access to most SVS Core Plus functionality via a Python scripting interface enabling you to automate workflows, interoperate with other programs, and develop more robust data management and manipulation routines. Also included is the mature statistical and numeric packages of NumPy and SciPy giving you a broad base of standardized test statistics to add your own methods as well as the 2D plotting library, matplotlib, for generating a near limitless number of publication quality plots and other visualizations.
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