Chiron is a tool for segmentation-free base-calling, using deep learning. Researchers can either use pre-trained models, or can use Chiron to learn new models.
Lachlan completed a Bachelor of Science at Australian National University, majoring in Mathematics. After several years out of science working in consulting, he went to the Wellcome Trust Sanger Institute, UK to complete a PhD in bioinformatics. Lachlan was a research fellow at the School of Public Health, Imperial College London, largely working on methodology for genome-wide association studies. He returned to Australia in 2012 to start a group at the Institute for Molecular Bioscience, University of Queensland where his group works on developing genomics and bioinformatics tools in infectious disease and cancer.
NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments. The core algorithm of NanoSV identifies split mapped reads and clusters the split-mapped orientations and genomic positions to identify breakpoint-junctions of structural variations.
Jose Espejo Valle-Inclan is a PhD student in the group of Wigard Kloosterman at the University Medical Center in Utrecht, Netherlands. His research centres on cancer genomics, particularly on ovarian cancer and focusing on the role and detection of structural variation. He holds a BSc in Biochemistry from the Autonomous University of Madrid, Spain and an MSc in Bioinformatics from the Wageningen University, Netherlands.
Pilon is a software program which takes a genome assembly along with sequencing reads aligned to it as input and analyzes the read data for evidence of differences between the sequencing and assembly. When used with sequencing data from the same organism aligned to a draft genome, Pilon will output an improved assembly after identifying and fixing several kinds of discrepancies. When used with sequencing data from a closely related organism aligned to a reference genome, Pilon will call variants, which can be output as a VCF file. Pilon has been available for several years, and has become a widely used tool for "polishing" draft assemblies created from less accurate long-read technologies by overlaying high quality short-read data to improve local base quality. I have recently started new development work to enhance Pilon to use long read data from Oxford Nanopore and PacBio sequencing directly, and I will demonstrate both the old and new capabilities.
Bruce Walker is Vice President of Technology at Applied Invention, as well as Visiting Scientist at the Broad Institute of MIT & Harvard, where he previously worked for over 10 years as Director of IT and Director of Genome Assembly and Analysis. Bruce holds a B.Sc. in Physics from MIT, and has spent most of his career developing scalable, high-performance computing architectures and algorithms.
Real-time selective sequencing with RUBRIC
Building upon the pioneering Read Until work of Matt Loose and his team, we have demonstrated an integrated real-time selective sequencing software architecture dubbed RUBRIC (Read Until with Basecall- and Reference-Informed Criteria). Unlike the event trace (“squiggle”) pattern matching approach previously described for Read Until, RUBRIC combines real-time basecalling and rapid, on-the-fly alignment to conventional ACTG reference sequences as the basis for molecule-by-molecule DNA selection and target enrichment. In addition to providing operational flexibility and scalability in choosing references for target selection, the RUBRIC system can be effectively implemented using off-the-shelf PCs rather than cluster computing platforms. We evaluate the performance of the RUBRIC method in detail, with particular attention to lessons learned in implementing this approach. We also assess the implications of fully optimized RUBRIC-based target enrichment for applications like point-of-care pathogen diagnostics and metagenomic analysis.
Dr. Michael Bartsch is a Principal Member of the Technical Staff in the Exploratory Engineering Solutions department at Sandia National Laboratories in Livermore, California. Before joining Sandia in 2005, Michael received a B.M.E from the University of Dayton, and M.S. and Ph.D. degrees in mechanical engineering from Stanford University. Dr. Bartsch has extensive, applied R&D experience leveraging microscale phenomena, high-resolution sensing, microfluidics, thermal analysis, microsystems engineering, and finite element modeling to address a variety of multidisciplinary applications and enable novel modes of scientific exploration. His most recent work has focused on applying highly integrated and automated microfluidic system architectures and innovative fluid manipulation technologies to problems in next-generation sequencing, DNA forensics, analytical chemistry, and materials science. Michael is currently the principal investigator of the Real-time Automated Pathogen Identification by Enhanced Ribotyping (RAPIER) project, an effort seeking to leverage the capabilities of the Oxford MinION nanopore sequencer for pathogen diagnostics.
Krishnakumar, R. et al. Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias. Scientific Reports 8, (2018)
Bartsch, M. S. et al. The rotary zone thermal cycler: A low-power system enabling automated rapid PCR. PLoS ONE 10, (2015)
Kim, H. et al. A microfluidic DNA library preparation platform for next-generation sequencing. PLoS ONE 8, (2013)
Jebrail, M. J., Bartsch, M. S. & Patel, K. D. Digital microfluidics: a versatile tool for applications in chemistry, biology and medicine. Lab Chip 12, 2452–2463 (2012)
Thaitrong, N. et al. Quality control of next-generation sequencing library through an integrative digital microfluidic platform. Electrophoresis 33, 3506–3513 (2012)
Kim, H. et al. Automated digital microfluidic sample preparation for next-generation DNA sequencing. Journal of Laboratory Automation 16, 405–414 (2011)
Tombo: detection of non-standard nucleotides using raw nanopore signal
Tombo is a suite of tools for the identification of modified nucleotides from nanopore sequencing data and visualization of raw nanopore signal. Tombo provides three methods for the investigation of DNA base modifications: specific alternative base detection, canonical (control) sample comparison and de novo canonical model comparison. In addition, Tombo includes a workflow for processing nanopore signal generated by direct RNA sequencing. The advantages and requirements for each detection method will be discussed.
Michael’s graduate and postdoctoral work at Portland State University and Oregon Health Sciences University focused on the biology of gene expression and regulation. Michael then worked as a senior scientific specialist for a leading next-generation sequencing company. He joined Oxford Nanopore Technologies in September 2014 as Technical Applications Manager. He is currently responsible for overseeing US technical support operations.
TractION is an open source LIMS written by the Production Software team at the Wellcome Sanger Institute. It provides tracking of library preparation and sequencing on the GridION platform.
Beth Flint is a Senior Scientific Manager at the Wellcome Sanger Institute, in Hinxton, South Cambs. She studied Computer Science at UCL and after graduating, started working as a software developer before eventually joining the Wellcome Sanger Institute. Here she has developed Laboratory Information Management Systems (LIMS) for their high throughput library preparation and NGS pipelines. Beth now manages the software development team responsible for developing LIMS in DNA pipelines at the Sanger.
Using MinKNOW to assess the quality of your run - The Duty Time Plot