Gene Myers, Director and Tschira Chair of Systems Biology, Max Planck Institute for Molecular Cell Biology and Genetics

Perfect Bacterial Genome Sequences Have Arrived
After a miserable decade of living with short read sequencers, the advent of long read sequencers such as the Pacbio Sequel have ushered in an era where one can expect to perfectly determine the genome of bacteria. Despite a 15% error rate in the raw reads, the final sequence can be as accurate as one error in 10-6 or 10-7 depending how deeply one is willing to sequence the target. We will discuss this new technology, the characteristics of the data, and the algorithms for assembly that produce these perfect reconstructions.

Bibliography

  • Real-Time DNA Sequencing from Single Polymerase Molecules. Science, 2009
  • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 2013
  • Efficient Alignment Discovery amongst Noisy Long Reads. WABI, 2014
  • A human gut microbial gene catalogue established by metagenomic sequencing.




    • Monitoring Bacteria on the Mother Machine
    Observing growing bacteria in fabricated nano-wells greatly simplifies the task of monitoring growing bacteria and is becoming a popular platform for such studies. Nonetheless, the problem of tracking the bacteria on such a “mother machine” is still quite interesting. Using an approach that selects a tracking over many possible segmentations of the data, we have built a very high-performance software system that further features “leveraged” user curation, i.e. giving one corrective clue can fix as many as a dozen errors in the automated result of the system. We are currently applying the machine with collaborators in Basel, and hope that by the time of the school we will further be able to discuss one or more biological findings.

    Bibliography

  • Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine. Bayesian and Graphical Models for Biomedical Imaging (Springer International Publishing), 2014
  • Tracking by assignment facilitates data curation. IMIC Workshop at MICCAI, 2014