Exploring science is typically characterized by a lot of puzzles, frustrations or even failures. This weblog is mainly intended to record my working, thinking and knowledge acquisitions. I expect that some reflection would refresh my mind from time to time, and motivate me to move further, and hopefully give me a better view about even changing the landscape of bioinformatics.
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Tuesday, May 3, 2011
Get SMRT: Pacific Biosciences Unveils Software Suite with Commercial Launch
April 29, 2011 | Third-generation sequencing company Pacific Biosciences (PacBio) began commercial shipment of its PacBio RS single-molecule sequencer this week. The instrument has been in beta testing at 11 institutions in North America and elsewhere for the past year. A notable success was the recent sequencing and identification of the cholera strain sweeping Haiti after the devastating 2010 earthquake.
In a briefing with Bio-IT World, PacBio staffers Kevin Corcoran, Jon Sorenson and Edwin Hauw previewed the new suite of software tools on the RS sequencer. The SMRT (single molecule/real time) Analysis software suite features web-based software, an analysis pipeline framework, and algorithms for sequence alignment and de novo assembly.
“We’re accelerating the development of software with the community,” says Kevin Corcoran. “A key feature of third-generation sequencing is that [the technology] doesn’t match up with what’s out there now. The key features of the PacBio system include fast time to result, high granularity, long read lengths, and new sequencing modes, including a circular mode and strobe sequencing.”
PacBio’s single-molecule sequencing system offers significantly longer read lengths (1,000 bases on average) than its second-generation sequencing rivals, and faster run times. That said, the total sequence throughput per run is currently less than other commercial platforms. The single-read accuracy hovers in the 85-90% range.
A revelatory feature of the SMRT software portal is that it captures kinetic information – the time for each registered nucleotide to be captured and incorporated into the growing DNA strand. “This is the first time you can watch DNA polymerase in real time, so that kinetic information will provide additional applications that have never been enabled before,” says Corcoran.
The genome browser is called SMRT View. “This takes advantage of our longer reads and kinetic information,” says Sorenson. It includes strobe and consensus sequence modes, allowing the user tovisualize and interact with secondary analysis sequence data. PacBio says the interactive graphical representations of variants, quality values, and other metrics is the first data visualization application that can visualize kinetics and structure information unique to PacBio's SMRT technology.