View Press Releases
Bam.iobio: An Interactive, Real-Time, Sequence Alignment Inspector App
SALT LAKE CITY - Nov 25, 2014 - Bam.iobio 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.
The ability to generate data on the scale of the entire genome at
ever-decreasing costs has taken the community by surprise, says
Marth. We want to make this data really useful to the researchers.
Were eliminating the need for expensive computational and hardware
investments that before had limited this type of analysis to
typically being done in institutional-scale data centers.
Bam.iobio will be the first of a series of apps to be developed
using the powerful IOBIO operating system. The second in
the series, vcf.iobio, 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.
The main IOBIO project
website is, http://iobio.io.
# # #
Listen to Gabor Marth explain bam.iobio and its features on the Scope Radio
Development of bam.iobio was supported by the National Human Genome Research Institute
BAM.IOBIO: A web-based, real-time, interactive sequence alignment file inspector application, appearing online in Nature Methods on Nov. 25, was authored by Chase Miller, Yi Qiao, and Gabor Marth of the department of human genetics and USTAR Center for Genetic Discovery at the University of Utah, and Brian DAstous formerly at Boston College, now at National Public Radio.