Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION TM sequencing

Keywords

Minion, Nanopore sequencing, Streaming algorithm, DNA sequencing, Identification (biology)

References

• Advances in Knowledge Discovery and Data MiningLai, Wei, Qian, Yu, Zhang, Kang — 2004
• Software Tools and Algorithms for Biological SystemsHamid R. Arabnia, Quôc-Nam Trân — 2013
• A complete bacterial genome assembled de novo using only nanopore sequencing dataNicholas J. Loman, Joshua Quick, Jared T. Simpson — 2015
• Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of SalmonellaJoshua Quick, Philip Ashton, Szymon Calus — 2015
• Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genesKim Judge, Simon R. Harris, Sandra Reuter — 2015
• MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance islandPhilip Ashton, Satheesh Nair, Tim Dallman — 2014
• Data streams: algorithms and applicationsS. Muthukrishnan — 2005
• Parameters for accurate genome alignmentMartin C. Frith, Michiaki Hamada, Paul Horton — 2010
• Improved data analysis for the MinION nanopore sequencerMiten Jain, Ian T. Fiddes, Karen H. Miga — 2015
• Finite-state models in the alignment of macromoleculesLloyd Allison, Christopher S. Wallace, C. N. Yee — 1992
• The Next-Generation Sequencing Revolution and Its Impact on GenomicsDaniel C. Koboldt, Karyn Meltz Steinberg, David E. Larson — 2013
• Parametric optimization of sequence alignmentDan Gusfield, Krishnakumar Balasubramanian, Dalit Naor — 1992
• Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males versus FemalesG. David Poznik, Brenna M. Henn, Muh-Ching Yee — 2013
• Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence TypingAlison J. Cody, Noel McCarthy, Melissa Jansen van Rensburg — 2013
• The potential and challenges of nanopore sequencingDaniel Branton, David W. Deamer, Andre Marziali — 2008
• A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencerJoshua Quick, Aaron R. Quinlan, Nicholas J. Loman — 2014
• A genome alignment algorithm based on compressionMinh Duc Cao, Trevor I. Dix, Lloyd Allison — 2010
• Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial IsolatesLaure Diancourt, Virginie Passet, J. Verhoef — 2005
• Bacterial genome sequencing in the clinic: bioinformatic challenges and solutionsW. Florian Fricke, David A. Rasko — 2013
• An Information Measure for ClassificationChristopher S. Wallace, D. M. Boulton — 1968

Cited by

• Sequencing ultra-long DNA molecules with the Oxford Nanopore MinIONJohn Urban, Jacob E. Bliss, Charles E. Lawrence — 2015
• Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencingMinh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott — 2015
• Realtime analysis and visualization of MinION sequencing data with npReaderMinh Duc Cao, Devika Ganesamoorthy, Matthew A. Cooper — 2016
• Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMapIvan Sović, Mile Šikić, Andreas Wilm — 2015
• Fast and sensitive mapping of nanopore sequencing reads with GraphMapIvan Sović, Mile Šikić, Andreas Wilm — 2016
• Scaffolding and completing genome assemblies in real-time with nanopore sequencingMinh Duc Cao, Son Hoang Nguyen, Devika Ganesamoorthy — 2016
• Next-generation sequencing diagnostics of bacteremia in septic patientsSilke Grumaz, Philip Stevens, Christian Grumaz — 2016
• Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility TestingYiyan Li, Xing Yang, Weian Zhao — 2017

Related papers

No related papers recorded.