Bam.iobio (http://bam.iobio.io) is the first app of its kind that allows scientists to analyze genome sequence data on their web browser, interactively, and in real-time, without having to rely on terabytes of storage and vast sources of computing power. The resource, developed by a team led by Gabor Marth, D.Sc., co-director of the USTAR Center for Genetic Discovery and human genetics professor at the University of Utah, appears online in the journal Nature Methods on Nov. 25.

The app analyzes BAM sequence alignment files, data generated from sequencing machines with detailed information on sequence quality and coverage. Ordinarily BAM interpretation takes hours or even longer to complete, and is encoded in an only machine-readable format. For the first time, bam.iobio puts this type of detailed inspection into the hands of the researcher. Data are expressed in a graphic interface that is easy-to-use and intuitive, enabling scientists to focus in on specific regions or genes of interest, if desired. The responsive format empowers the user to customize analysis parameters on the fly, returning query results in real-time.

Bam.iobio will be the first of a series of apps to be developed using the powerful IOBIO (http://iobio.io) "operating system". The second in the series, vcf.iobio (http://vcf.iobio.io), is also ready to use and enables scientists to analyze genomic variant report files – data on single nucleotide polymorphism and structural genetic variants - interactively, and in real-time. In the future, the team plans to develop apps for interactive, custom gene annotation, for examining local ancestry in a patient genome, and other interactive genome analyses. The next phase of the project, to occur within the next three months, will be a release of software libraries to developers so they can create their own apps based on the IOBIO platform.

Try bam.iobio: Go to http://bam.iobio.io, click "Choose Bam Url", and then "go" next to the default url.
Try vcf.iobio: Go to http://vcf.iobio.io, click on "Choose VCF Url", and then "go" next to the default url.
IOBIO project website: http://iobio.io.

Development of bam.iobio was supported by the National Human Genome Research Institute

Listen to Gabor Marth explain bam.iobio and its features: http://healthcare.utah.edu/the-scope/shows.php?shows=0_djpfw8ee

ARTICLE

BAM.IOBIO: A web-based, real-time, interactive sequence alignment file inspector application; Chase A Miller, Yi Qiao, Tonya DiSera, Brian D'Astous, and Gabor T Marth; Nature Methods, published online November 25, 2014 http://www.nature.com/nmeth/journal/v11/n12/full/nmeth.3174.html