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PacBio long read sequencer for the Ramaciotti Genomics Consortium of NSW

Project Member(s): Djordjevic, S., Bhattacharya, P.

Funding or Partner Organisation: Australian Research Council (ARC Linkage Infrastructure)

Start year: 2015

Summary: The Ramaciotti Centre for Genomics is a consortium of NSW-based universities and research institutes. It is the technical focus for genomics and transcriptomics expertise in NSW. In 2013 it analysed 2,974 samples by next-generation sequencing, 2,535 samples by microarray and analysed 54,936 samples by capillary sequencing. This LIEF proposal requests a PacBio long-read sequencer. Unlike other next-generation sequencers, that have read lengths of 100 to 700 bases, it generates an average read length of 8,000 bases and maximum of 20,000 bases. If funded, this will be the first PacBio for a service facility in Australia. It will be used by the CIs, and the user base of the Centre, for research in genomics, metagenomics and transcriptomics.

Publications:

Cummins, ML, Reid, CJ, Roy Chowdhury, P, Bushell, RN, Esbert, N, Tivendale, KA, Noormohammadi, AH, Islam, S, Marenda, MS, Browning, GF, Markham, PF & Djordjevic, SP 2019, 'Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene.', Microbial genomics, vol. 5, no. 2.
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Monahan, LG, DeMaere, MZ, Cummins, ML, Djordjevic, SP, Roy Chowdhury, P & Darling, AE 2019, 'High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei.', Gut pathogens, vol. 11, no. 1.
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Roy Chowdhury, P, McKinnon, J, Liu, M & Djordjevic, SP 2019, 'Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location.', Frontiers in microbiology, vol. 9, no. Jan, pp. 3212-3212.
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Wyrsch, ER, Hawkey, J, Judd, LM, Haites, R, Holt, KE, Djordjevic, SP & Billman-Jacobe, H 2019, 'Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production.', Microorganisms, vol. 7, no. 9.
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Wyrsch, ER, Reid, CJ, DeMaere, MZ, Liu, MY, Chapman, TA, Roy Chowdhury, P & Djordjevic, SP 2019, 'Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia', Frontiers in Sustainable Food Systems, vol. 3.
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McKinnon, J, Roy Chowdhury, P & Djordjevic, SP 2018, 'Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis.', International journal of antimicrobial agents, vol. 52, no. 3, pp. 430-435.
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O'Rourke, MB, Djordjevic, SP & Padula, MP 2018, 'The Quest for Improved Reproducibility In MALDI Mass Spectrometry', Mass Spectrometry Reviews, vol. 37, no. 2, pp. 217-228.
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Wyrsch, E, Roy Chowdhury, P, Chapman, TA, Charles, IG, Hammond, JM & Djordjevic, SP 2016, 'Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis', Frontiers in Microbiology, vol. 7, no. 843.
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Keywords: genomics, transcriptomics

FOR Codes: Genomics, Genome Structure and Regulation, Expanding Knowledge in the Biological Sciences