Neptune: A bioinformatics tool for rapid discovery of genomic variation in bacterial populations

Nucleic Acids Research

Volumn 45, Issue 18, 2017, Pages

  Marinier, Eric ^a   Zaheer, Rahat ^a,n   Berry, Chrystal ^a   Weedmark, Kelly A ^a,f   Domaratzki, Michael ^b   Mabon, Philip ^a   Knox, Natalie C ^a   Reimer, Aleisha R ^a   Graham, Morag R ^a,b   Chui, Linda ^c,d   Patterson Fortin, Laura ^d,o   Zhang, Jian ^e   Pagotto, Franco ^f   Farber, Jeff ^f,p   Mahony, Jim ^g   Seyer, Karine ^h   Bekal, Sadjia ^i,j   Tremblay, Cécile ^i,j,q   Isaac Renton, Judy ^k,l   Prystajecky, Natalie ^k,l   Chen, Jessica ^l,r   Slade, Peter ^m,s   Van Domselaar, Gary ^a,b   more..

^a PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^b UNIVERSITY OF MANITOBA   (Canada)

^c PROVINCIAL LABORATORY FOR PUBLIC HEALTH   (Canada)

^d UNIVERSITY OF ALBERTA   (Canada)

^e ALBERTA INNOVATES TECHNOLOGY FUTURES   (Canada)

^f HEALTH CANADA   (Canada)

^g MCMASTER UNIVERSITY   (Canada)

^h CANADIAN FOOD INSPECTION AGENCY   (Canada)

ⁱ INSTITUT NATIONAL DE SANTÉ PUBLIQUE DU QUÉBEC   (Canada)

^j UNIVERSITÉ DE MONTRÉAL   (Canada)

^k BCCDC Public Health Microbiology and Reference Laboratory   (Canada)

^l UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^m Maple Leaf Foods   (Canada)

ⁿ LETHBRIDGE RESEARCH CENTRE   (Canada)

^o BioLargo Water Inc   (Canada)

^p UNIVERSITY OF GUELPH   (Canada)

^q CENTRE HOSPITALIER DE L UNIVERSITÉ DE MONTRÉAL   (Canada)

^r CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^s Food Policy Consultant   (Canada)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BIOINFORMATICS; COMPARATIVE STUDY; CONTROLLED STUDY; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC TRAIT; GENETIC VARIATION; GENOMICS; NONHUMAN; PATHOGENOMICS; PRIORITY JOURNAL; PROBABILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SIMULATION; SOFTWARE; STATISTICAL MODEL; BACILLUS ANTHRACIS; BACTERIUM; BIOLOGY; DNA MUTATIONAL ANALYSIS; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION STUDY; GENETICS; MICROBIOLOGICAL EXAMINATION; PROCEDURES; VALIDATION STUDY; VIBRIO CHOLERAE;

TRANSCRIPTOME;

BACILLUS ANTHRACIS; BACTERIA; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC ASSOCIATION STUDIES; GENOME, BACTERIAL; MICROBIOLOGICAL TECHNIQUES; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTOME; VIBRIO CHOLERAE;

EID: 85032474600     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx702     Document Type: Article

References (27)

1. Davis, S., Pettengill, J. B., Luo, Y., Payne, J., Shpuntoff, A., Rand, H. and Strain, E. (2015) CFSAN SNP pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Comput. Sci., 1, e20.
2. Sahl, J. W., Lemmer, D., Travis, J., Schupp, J. M., Gillece, J. D., Aziz, M., Driebe, E. M., Drees, K. P., Hicks, N. D., Williamson, C. H. D. et al. (2016) NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb. Genom., 2, e000074.
3. Gao, L. and Qi, J. (2007) Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol. Biol., 7, 41-47.
4. Ondov, B. D., Treangen, T. J., Melsted, P., Mallonee, A. B., Bergman, N. H., Koren, S. and Phillippy, A. M. (2016) Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol., 17, 132-145.
5. Sims, G. E. and Kim, S.-H. (2011) Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc. Natl. Acad. Sci. U. S. A., 108, 8329-8334.
6. Earle, S. G., Wu, C.-H., Charlesworth, J., Stoesser, N., Gordon, N. C., Walker, T. M., Spencer, C. C. A., Iqbal, Z., Clifton, D. A., Hopkins, K. L. et al. (2016) Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat. Microbiol., 1, 16041-16061.
7. Lees, J. A., Vehkala, M., Välimäki, N., Harris, S. R., Chewapreecha, C., Croucher, N. J., Marttinen, P., Davies, M. R., Steer, A. C., Tong, S. Y. C. et al. (2016) Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nat. Commun., 7, 12797-12804.
8. Slezak, T., Kuczmarski, T., Ott, L., Torres, C., Medeiros, D., Smith, J., Truitt, B., Mulakken, N., Lam, M., Vitalis, E. et al. (2003) Comparative genomics tools applied to bioterrorism defence. Brief. Bioinform., 4, 133-149.
9. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
10. Phillippy, A. M., Ayanbule, K., Edwards, N. J. and Salzberg, S. L. (2009) Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Res., 37(Suppl. 2), W229-W234.
11. Bader, K. C., Grothoff, C. and Meier, H. (2011) Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets. Bioinformatics, 27, 1546-1554.
12. Satya, R. V., Zavaljevski, N., Kumar, K. and Reifman, J. (2008) A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinform., 9, 185-197.
13. Satya, R. V., Kumar, K., Zavaljevski, N. and Reifman, J. (2010) A high-throughput pipeline for the design of real-time PCR signatures. BMC Bioinform., 11, 340-349.
14. Melsted, P. and Pritchard, J. K. (2011) Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinform., 12, 333-339.
15. Feller, V. (1960) An Introduction to Probability Theory and Its Applications. J. Wiley & Sons, NY, Vol. 1.
16. Dhillon, B. K., Laird, M. R., Shay, J. A., Winsor, G. L., Lo, R., Nizam, F., Pereira, S. K., Waglechner, N., McArthur, A. G., Langille, M. G. et al. (2015) IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res., 43, W104-W108.
17. Petkau, A., Stuart-Edwards, M., Stothard, P. and Van Domselaar, G. (2010) Interactive microbial genome visualization with GView. Bioinformatics, 26, 3125-3126.
18. Orsi, R. H., den Bakker, H. C. and Wiedmann, M. (2011) Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics. Int. J. Med. Microbiol, 301, 79-96.
19. Gilmour, M. W., Graham, M., Van Domselaar, G, Tyler, S., Kent, H., Trout-Yakel, K. M., Larios, O., Allen, V, Lee, B. and Nadon, C. (2010) High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics, 11, 120-134.
20. Bierne, H., Sabet, C., Personnic, N. and Cossart, P (2007) Internalins: a complex family of leucine-rich repeat-containing proteins in Listeria monocytogenes. Microb. Infect., 9, 1156-1166.
21. C and LstR, a lineage II-specific heat shock system. J. Bacteriol, 187, 7243-7253.
22. Shao, Y., He, X., Harrison, E. M., Tai, C., Ou, H.-Y, Rajakumar, K. and Deng, Z. (2010) mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Nucleic Acids Res., 38(Suppl. 2), W194-W200.
23. Laing, C., Buchanan, C., Taboada, E. N., Zhang, Y., Kropinski, A., Villegas, A., Thomas, J. E. and Gannon, V. P (2010) Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinform., 11, 461-474.
24. Koskiniemi, S., Lamoureux, J. G, Nikolakakis, K. C, de Roodenbeke, C.t., Kaplan, M. D., Low, D. A. and Hayes, C. S. (2013) RHS proteins from diverse bacteria mediate intercellular competition. Proc. Nati. Acad. Sci. U. S. A., 110, 7032-7037.
25. Carvalho, F., Sousa, S. and Cabanes, D. (2014) How Listeria monocytogenes organizes its surface for virulence. Front. Cell. Infect. Microbiol., 4, 48-69.
26. Cotter, P. D., Draper, L. A., Lawton, E. M., Daly, K. M., Groeger, D. S., Casey, P. G., Ross, R. P and Hill, C. (2008) Listeriolysin S, a novel peptide haemolysin associated with a subset of lineage I Listeria monocytogenes. PLoSPathog., 4, e1000144.
27. Maury, M. M., Tsai, Y.-H., Charlier, C., Touchon, M., Chenal-Francisque, V, Leclercq, A., Criscuolo, A., Gaultier, C., Roussel, S., Brisabois, A. et al. (2016) Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat. Genet., 48, 308-313.