Genome Browsers: 4 Free Bioinformatic Software Tools
Articles —> Genome Browsers: 4 Free Bioinformatic Software Tools
Given the scale of information they contain, large scale sequences - in particular genomes and genome annotations - are difficult to analyze without a comprehensive visualization tool such as a genome browser. Some more frequently studied organisms have public resources and genome browsers available to view and analyze their respective genomes. For example, Saccharomyces cerevisiae's SGD and Homo sapiens UCSC Genome Browser. However many organisms or variants of organisms do not have publicly available resources, thus analyzing and visualizing the genome may be a bit more complex. There are commercial solutions available, but what is available in the public domain for free? Below I outline four publicly available tools to visualize and browse genomic sequences.
Integrative Genome Browser (IGV).
IGV is a free by the Broad institute. IGV is a complete genome browser and, as opposed to the public resources above which run through a web browser, IGV is run as a stand-alone application a feature which can make any application much more usable and dynamic.
IGV is written in Java, making it cross-platform compatible. The software recognizes several common genome and next gen sequencing file formats, including GFF and the common next-gen sequencing formats BAM, SAM, and VCF - a useful feature in that one can view both genome annotation as well as next-gen sequencing results. Loading, browsing, and studying the annotation is relatively easy. Further, IGV provides a network interface which provides the capability to operate the program via networking - useful if one wishes to communicate between applications or automate tasks in the software. All together IGV is a great tool to view genomes, compare alignments, or look at raw next-gen sequencing reads aligned to a reference.
JBrowse
JBrowse is a genome browser written in javascript for viewing genomes within a web browser. JBrowse runs within a web browser and supports a variety of web browsers and data file formats.
JBrowse is easy to use, providing a scrollable user interface to visualize annotated sequences and genomes. However installation and configuration requires scripting and website design knowledge. Further, users of JBrowse will be required to set up their genomes locally or on a separate shared server, further requiring scripting and command line knowledge. Thus JBrowse is not a click and go type of software - the activation energy to get JBrowse up and running is high. That being said the usefulness is in its capability to readily share an annotation or genome with a group of people.
GBrowse
GBrowse is an open source project whose API is used by several public database, such as Wormbase and Flybase. This tool is similar in concept to JBrowse in that it runs through a web browser. However its technology is a bit different and a bit more complex relative to JBrowser. Setup requires some knowledge of software and web design, and while JBrowse is predominantly javascript GBrowse uses server side scripting (Perl). From a user's perspective GBrowse is intuitive, and gives a user good overall control for genome browsing. Similar to JBrowse, GBrowse inherently has the capability to share genome and genome annotations with a group of people.
NCBI Genome Workbench
NCBI Genome Workbench is a stand-alone genome browser software package provided for free by the National Center for Biotechnology Information (NCBI). The NCBI Genome Workbench is a comprehensive tool, with visualization capability as well as the capability to retrieve sequences from NCBI - one of the most comprehensive biological sequence databases available. Similar to IGV, the workbench provides a scrollable view of a genome and or sequence as well as compatibility with a large number of file formats and is supported on many different operating systems.
Conclusions
Although there is overlap between many of these tools insofar as their capability, each has a particular niche it fills. IGV is an empty box useful for scientists to view annotated sequences and genomes, as well as read mapping. While there is much overlap in functionality to the NCBI Genome Workbench, the NCBI Genome Workbench targets an audience wishing to access public databases. For example, while viewing an aligned BAM file to a reference in IGV is fairly straight forward, NCBI Genome Workbench relies heavily on public genomes as a reference making this process difficult (I have yet to find a solution1). Lastly, JBrowse and GBrowse accomplish the task which is difficult (but not impossible) to do with the other tools: that is to share an annotated sequence or genome across a group.
More Options
While the above four tools are popular to use, there are other genome browsers not listed but worth trying out. My experience is less than ideal, but everyone's mileage may very. These include:
- Argo - another java stand-alone application from Broad, in my opinion it's user interface and customization options are not as ideal as IGV or NCBI Genome Workbench.1
- Artemus - a Genome browser offering from the Wellcome Trust Sanger Institute, Artemus is another stand alone application written in Java. Relative to the three applications above, I've personally found it's user interface a bit harder to use (for example, a vertical scroll bar to zoom).
1As of this writing
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