Primer on infectious disease bacterial genomics

Clinical Microbiology Reviews

Volumn 29, Issue 4, 2016, Pages 881-913

  Lynch, Tarah ^a,b   Petkau, Aaron ^c   Knox, Natalie ^c   Graham, Morag ^c,d   Van Domselaar, Gary ^c,d  

^a CALGARY LABORATORY SERVICES   (Canada)

^b UNIVERSITY OF CALGARY   (Canada)

^c PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^d UNIVERSITY OF MANITOBA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL GENETICS; BACTERIAL INFECTION; BIOINFORMATICS; CLOUD COMPUTING; GENE SEQUENCE; GENETIC RECOMBINATION; HIGH THROUGHPUT SEQUENCING; HOMOLOGOUS RECOMBINATION; MOLECULAR GENETICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; PROPHAGE; SCORING SYSTEM; SEQUENCE ALIGNMENT; TRANSPOSON; BACTERIAL GENOME; COMMUNICABLE DISEASE; GENETICS; GENOMICS; HUMAN; MICROBIOLOGY;

COMMUNICABLE DISEASES; GENOME, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS;

EID: 84986628152     PISSN: 08938512     EISSN: 10986618     Source Type: Journal    
DOI: 10.1128/CMR.00001-16     Document Type: Article

References (249)

1. Portny SE, Austin J. 12 July 2002. Project management for scientists. American Association for the Advancement of Science, Washington, DC. http://www.sciencemag.org/careers/2002/07/project-management-scientists
2. Sandve GK, Nekrutenko A, Taylor J, Hovig E. 2013. Ten simple rules for reproducible computational research. PLoS Comput Biol 9:e1003285. http://dx.doi.org/10.1371/journal.pcbi.1003285
3. Vos RA. 2016. Ten simple rules for managing high-throughput nucleotide sequencing data. bioRxiv http://dx.doi.org/10.1101/049338
4. Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D. 2012. The Metadata Coverage Index (MCI): a standardized metric for quantifying database metadata richness. Stand Genomic Sci 6:438–447. http://dx.doi.org/10.4056/sigs.2675953
5. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmuller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM. 2012. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 30:1033–1036. http://dx.doi.org/10.1038/nbt.2403
6. Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA, Murch RS, Sajantila A, Schmedes SE, Ternus KL, Turner SD, Minot S. 2014. Validation of high throughput sequencing and microbial forensics applications. Investig Genet 5:9. http://dx.doi.org/10.1186/2041-2223-5-9
7. Kell DB, Oliver SG. 2004. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 26:99–105. http://dx.doi.org/10.1002/bies.10385
8. Junemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D. 2014. GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS One 9:e107014. http://dx.doi.org/10.1371/journal.pone.0107014
9. Kodama Y, Shumway M, Leinonen R. 2012. The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res 40:D54–D56. http://dx.doi.org/10.1093/nar/gkr854
10. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/ Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771. http://dx.doi.org/10.1093/nar/gkp1137
11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. http://dx.doi.org/10.1093/bioinformatics/btp352
12. Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. 2011. The sequence read archive. Nucleic Acids Res 39:D19–D21. http://dx.doi.org/10.1093/nar/gkq1019
13. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
14. Fusaro VA, Patil P, Gafni E, Wall DP, Tonellato PJ. 2011. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol 7:e1002147. http://dx.doi.org/10.1371/journal.pcbi.1002147
15. Angiuoli SV, White JR, Matalka M, White O, Fricke WF. 2011. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS One 6:e26624. http://dx.doi.org/10.1371/journal.pone.0026624
16. Shanahan HP, Owen AM, Harrison AP. 2014. Bioinformatics on the cloud computing platform Azure. PLoS One 9:e102642. http://dx.doi.org/10.1371/journal.pone.0102642
17. Nosowsky R, Giordano TJ. 2006. The Health Insurance Portability and Accountability Act of 1996 (HIPAA) privacy rule: implications for clinical research. Annu Rev Med 57:575–590. http://dx.doi.org/10.1146/annurev.med.57.121304.131257
18. Griebel L, Prokosch HU, Kopcke F, Toddenroth D, Christoph J, Leb I, Engel I, Sedlmayr M. 2015. A scoping review of cloud computing in healthcare. BMC Med Inform Decis Mak 15:17. http://dx.doi.org/10.1186/s12911-015-0145-7
19. Rodriguez LL, Brooks LD, Greenberg JH, Green ED. 2013. Research ethics. the complexities of genomic identifiability. Science 339:275–276. http://dx.doi.org/10.1126/science.1234593
20. Luheshi L, Raza S, Moorthie S, Hall A, Blackburn L, Rands C, Sagoo G, Chowdhury S, Kroese M, Burton H. 2015. Pathogen genomics into practice. PHG Foundation, Cambridge, United Kingdom
21. Allard MW, Strain E, Melka D, Bunning K, Musser SM, Brown EW, Timme R. 2016. Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J Clin Microbiol 54:1975–1983. http://dx.doi.org/10.1128/JCM.00081-16
22. Dove ES, Joly Y, Tasse AM, Public Population Project in Genomics and Society (P3G) International Steering Committee, International Cancer Genome Consortium (ICGC) Ethics and Policy Committee, Knoppers BM. 2015. Genomic cloud computing: legal and ethical points to consider. Eur J Hum Genet 23:1271–1278. http://dx.doi.org/10.1038/ejhg.2014.196
23. Wyres KL, Conway TC, Garg S, Queiroz C, Reumann M, Holt K, Rusu LI. 2014. WGS analysis and interpretation in clinical and public health microbiology laboratories: what are the requirements and how do existing tools compare? Pathogens 3:437–458. http://dx.doi.org/10.3390/pathogens3020437
24. Goecks J, Nekrutenko A, Taylor J, Galaxy Team. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11:R86. http://dx.doi.org/10.1186/gb-2010-11-8-r86
25. Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N Galaxy Team, Taylor J, Nekrutenko A. 2014. Dissemination of scientific software with Galaxy ToolShed. Genome Biol 15:403. http://dx.doi.org/10.1186/gb4161
26. Afgan E, Chapman B, Taylor J. 2012. CloudMan as a platform for tool, data, and analysis distribution. BMC Bioinformatics 13:315. http://dx.doi.org/10.1186/1471-2105-13-315
27. Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A. 2015. Genomics virtual laboratory: a practical bioinformatics workbench for the cloud. PLoS One 10:e0140829. http://dx.doi.org/10.1371/journal.pone.0140829
28. Liu B, Madduri RK, Sotomayor B, Chard K, Lacinski L, Dave UJ, Li J, Liu C, Foster IT. 2014. Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses. J Biomed Inform 49:119–133. http://dx.doi.org/10.1016/j.jbi.2014.01.005
29. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75
30. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Ponten T, Ussery DW, Aarestrup FM, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. http://dx.doi.org/10.1128/JCM.06094-11
31. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. http://dx.doi.org/10.1093/jac/dks261
32. Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. 2014. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One 9:e104984. http://dx.doi.org/10.1371/journal.pone.0104984
33. Jasny BR, Chin G, Chong L, Vignieri S. 2011. Data replication & reproducibility. Again, and again, and again…. Introduction. Science 334:1225. http://dx.doi.org/10.1126/science.334.6060.1225
34. Peng RD. 2011. Reproducible research in computational science. Science 334:1226–1227. http://dx.doi.org/10.1126/science.1213847
35. Nekrutenko A, Taylor J. 2012. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat Rev Genet 13:667–672. http://dx.doi.org/10.1038/nrg3305
36. Morrison SS, Pyzh R, Jeon MS, Amaro C, Roig FJ, Baker-Austin C, Oliver JD, Gibas CJ. 2014. Impact of analytic provenance in genome analysis. BMC Genomics 15(Suppl 8):S1. http://dx.doi.org/10.1186/1471-2164-15-S8-S1
37. Pightling AW, Petronella N, Pagotto F. 2014. Choice of reference sequence and assembler for alignment of Listeria monocytogenes shortread sequence data greatly influences rates of error in SNP analyses. PLoS One 9:e104579. http://dx.doi.org/10.1371/journal.pone.0104579
38. Mardis ER. 2013. Next-generation sequencing platforms. Annu Rev Anal Chem 6:287–303. http://dx.doi.org/10.1146/annurev-anchem-062012-092628
39. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. 2012. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364. http://dx.doi.org/10.1155/2012/251364
40. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ. 2012. Performance comparison of benchtop highthroughput sequencing platforms. Nat Biotechnol 30:434–439. http://dx.doi.org/10.1038/nbt.2198
41. Kwong JC, McCallum N, Sintchenko V, Howden BP. 2015. Whole genome sequencing in clinical and public health microbiology. Pathology 47:199–210. http://dx.doi.org/10.1097/PAT.0000000000000235
42. Glenn TC. 2011. Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759–769. http://dx.doi.org/10.1111/j.1755-0998.2011.03024.x
43. Koren S, Phillippy AM. 2015. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 23:110–120. http://dx.doi.org/10.1016/j.mib.2014.11.014
44. Loman NJ, Quick J, Simpson JT. 2015. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12:733–735. http://dx.doi.org/10.1038/nmeth.3444
45. Sit CS, Ruzzini AC, Van Arnam EB, Ramadhar TR, Currie CR, Clardy J. 2015. Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants. Proc Natl Acad Sci U S A 112:13150–13154. http://dx.doi.org/10.1073/pnas.1515348112
46. Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, Stryke D, Bouquet J, Somasekar S, Linnen JM, Dodd R, Mulembakani P, Schneider BS, Muyembe-Tamfum JJ, Stramer SL, Chiu CY. 2015. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 7:99. http://dx.doi.org/10.1186/s13073-015-0220-9
47. McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS. 2014. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highlyrepetitive transposable elements. PLoS One 9:e106689. http://dx.doi.org/10.1371/journal.pone.0106689
48. Nagarajan N, Pop M. 2010. Sequencing and genome assembly using next-generation technologies. Methods Mol Biol 673:1–17. http://dx.doi.org/10.1007/978-1-60761-842-3_1
49. Fox EJ, Reid-Bayliss KS, Emond MJ, Loeb LA. 2014. Accuracy of next generation sequencing platforms. Next Gener Seq Appl 1:1000106
50. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341. http://dx.doi.org/10.1186/1471-2164-13-341
51. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. 2014. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 15:121–132. http://dx.doi.org/10.1038/nrg3642
52. Robasky K, Lewis NE, Church GM. 2014. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet 15:56–62. http://dx.doi.org/10.1038/nrg3655
53. Lander ES, Waterman MS. 1988. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2:231–239
54. Green MR, Sambrook J. 2012. Molecular cloning: a laboratory manual, 4th ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
55. Centers for Disease Control and Prevention. 14 June 2013. Next generation sequencing: standardization of clinical testing (Nex-StoCT) working groups. Division of Laboratory Science and Standards, Office of Public Health Scientific Services, Centers for Disease Control and Prevention, Atlanta, GA. http://www.cdc.gov/ophss/csels/dls/glp_genetic_testing/nex-stoct.html
56. Tong W, Ostroff S, Blais B, Silva P, Dubuc M, Healy M, Slikker W. 2015. Genomics in the land of regulatory science. Regul Toxicol Pharmacol 72:102–106. http://dx.doi.org/10.1016/j.yrtph.2015.03.008
57. Global Microbial Identifer. 27 June 2016. Global Microbial Identifier consortium work group 4: ring trials and quality assurance. Global Microbial Identifier. http://www.globalmicrobialidentifier.org/Workgroups#work-group-4
58. Moran-Gilad J, Sintchenko V, Pedersen SK, Wolfgang WJ, Pettengill J, Strain E, Hendriksen RS, Global Microbial Identifier Initiative’s Working Group 4 (GMI-WG4). 2015. Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities. BMC Infect Dis 15:174. http://dx.doi.org/10.1186/s12879-015-0902-3
59. Paszkiewicz KH, Farbos A, O’Neill P, Moore K. 2014. Quality control on the frontier. Front Genet 5:157. http://dx.doi.org/10.3389/fgene.2014.00157
60. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. http://dx.doi.org/10.1093/bioinformatics/btu170
61. Li YL, Weng JC, Hsiao CC, Chou MT, Tseng CW, Hung JH. 2015. PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. BMC Bioinformatics 16(Suppl 1):S2. http://dx.doi.org/10.1186/1471-2105-16-S1-S2
62. Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. 2013. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One 8:e85024. http://dx.doi.org/10.1371/journal.pone.0085024
63. Yun S, Yun S. 2014. Masking as an effective quality control method for next-generation sequencing data analysis. BMC Bioinformatics 15:382. http://dx.doi.org/10.1186/s12859-014-0382-2
64. Liu Q, Guo Y, Li J, Long J, Zhang B, Shyr Y. 2012. Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data. BMC Genomics 13(Suppl 8):S8. http://dx.doi.org/10.1186/1471-2164-13-S8-S8
65. Chen T, Gan R, Chang Y, Liao W, Wu TH, Lee C, Huang P, Lee C, Chen YM, Chiu C, Tang P. 2015. Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing. BMC Genomics 16:648. http://dx.doi.org/10.3389/fgene.2014.00157
66. Martin M. 2011. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet J 17(1):10–12. http://dx.doi.org/10.14806/ej.17.1.200
67. Mukherjee S, Huntemann M, Ivanova N, Kyrpides NC, Pati A. 2015. Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Stand Genomic Sci 10:18. http://dx.doi.org/10.1186/1944-3277-10-18
68. Schmieder R, Edwards R. 2011. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6:e17288. http://dx.doi.org/10.1371/journal.pone.0017288
69. Hadfield J, Eldridge MD. 2014. Multi-genome alignment for quality control and contamination screening of next-generation sequencing data. Front Genet 5:31. http://dx.doi.org/10.3389/fgene.2014.00031
70. Zhou Q, Su X, Wang A, Xu J, Ning K. 2013. QC-chain: fast and holistic quality control method for next-generation sequencing data. PLoS One 8:e60234. http://dx.doi.org/10.1371/journal.pone.0060234
71. McNair K, Edwards RA. 2015. GenomePeek—an online tool for prokaryotic genome and metagenome analysis. PeerJ 3:e1025. http://dx.doi.org/10.7717/peerj.1025
72. Wood DE, Salzberg SL. 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15:R46. http://dx.doi.org/10.1186/gb-2014-15-3-r46
73. Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993. http://dx.doi.org/10.1093/bioinformatics/btr509
74. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group. 2011. The variant call format and VCFtools. Bioinformatics 27:2156–2158. http://dx.doi.org/10.1093/bioinformatics/btr330
75. Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z. 2014. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform 15:256–278. http://dx.doi.org/10.1093/bib/bbs086
76. Caboche S, Audebert C, Lemoine Y, Hot D. 2014. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data. BMC Genomics 15:264. http://dx.doi.org/10.1186/1471-2164-15-264
77. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. 2013. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43:11.10.1–11.10.33. http://dx.doi.org/10.1002/0471250953.bi1110s43
78. Li H. 2014. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 30:2843–2851. http://dx.doi.org/10.1093/bioinformatics/btu356
79. Treangen TJ, Salzberg SL. 2011. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13: 36–46. http://dx.doi.org/10.1038/nrg3117
80. Periwal V, Scaria V. 2015. Insights into structural variations and genome rearrangements in prokaryotic genomes. Bioinformatics 31:1–9. http://dx.doi.org/10.1093/bioinformatics/btu600
81. Wendl MC, Wilson RK. 2009. Statistical aspects of discerning indel-type structural variation via DNA sequence alignment. BMC Genomics 10: 359. http://dx.doi.org/10.1186/1471-2164-10-359
82. Fonseca NA, Rung J, Brazma A, Marioni JC. 2012. Tools for mapping high-throughput sequencing data. Bioinformatics 28:3169–3177. http://dx.doi.org/10.1093/bioinformatics/bts605
83. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359. http://dx.doi.org/10.1038/nmeth.1923
84. Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589–595. http://dx.doi.org/10.1093/bioinformatics/btp698
85. Thorvaldsdottir H, Robinson JT, Mesirov JP. 2013. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192. http://dx.doi.org/10.1093/bib/bbs017
86. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER. 2009. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681. http://dx.doi.org/10.1038/nmeth.1363
87. Olson ND, Lund SP, Colman RE, Foster JT, Sahl JW, Schupp JM, Keim P, Morrow JB, Salit ML, Zook JM. 2015. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. Front Genet 6:235. http://dx.doi.org/10.3389/fgene.2015.00235
88. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80–92. http://dx.doi.org/10.4161/fly.19695
89. Reumerman RA, Tucker NP, Herron PR, Hoskisson PA, Sangal V. 2013. Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes. Antonie Van Leeuwenhoek 104:431–434. http://dx.doi.org/10.1007/s10482-013-9953-x
90. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. http://dx.doi.org/10.1101/gr.107524.110
91. Simpson JT, Pop M. 2015. The theory and practice of genome sequence assembly. Annu Rev Genomics Hum Genet 16:153–172. http://dx.doi.org/10.1146/annurev-genom-090314-050032
92. Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for nextgeneration sequencing data. Genomics 95:315–327. http://dx.doi.org/10.1016/j.ygeno.2010.03.001
93. Ekblom R, Wolf JB. 2014. A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 7:1026–1042. http://dx.doi.org/10.1111/eva.12178
94. Nagarajan N, Pop M. 2013. Sequence assembly demystified. Nat Rev Genet 14:157–167. http://dx.doi.org/10.1038/nrg3367
95. Sutton GG, White O, Adams MD, Kerlavage AR. 1995. TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci Technol 1:9–19. http://dx.doi.org/10.1089/gst.1995.1.9
96. Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M. 2011. Next generation sequence assembly with AMOS. Curr Protoc Bioinformatics Chapter 11:Unit 11.8. http://dx.doi.org/10.1002/0471250953.bi1108s33
97. Chaisson MJ, Pevzner PA. 2008. Short read fragment assembly of bacterial genomes. Genome Res 18:324–330. http://dx.doi.org/10.1101/gr.7088808
98. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. http://dx.doi.org/10.1101/gr.074492.107
99. Simpson JT, Durbin R. 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 22:549–556. http://dx.doi.org/10.1101/gr.126953.111
100. Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 18:802–809. http://dx.doi.org/10.1101/gr.072033.107
101. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. http://dx.doi.org/10.1038/nmeth.2474
102. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18. http://dx.doi.org/10.1186/2047-217X-1-18
103. Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS. 2011. Efficient de novo assembly of single-cell bacterial genomes from shortread data sets. Nat Biotechnol 29:915–921. http://dx.doi.org/10.1038/nbt.1966
104. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to singlecell sequencing. J Comput Biol 19:455–477. http://dx.doi.org/10.1089/cmb.2012.0021
105. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B. 2011. A practical comparison of de novo genome assembly software tools for nextgeneration sequencing technologies. PLoS One 6:e17915. http://dx.doi.org/10.1371/journal.pone.0017915
106. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 21:2224–2241.http://dx.doi.org/10.1101/gr.126599.111
107. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. 2013. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2:10. http://dx.doi.org/10.1186/2047-217X-2-10
108. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Mar˜A§ais G, Pop M, Yorke JA. 2012. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22:557–567. http://dx.doi.org/10.1101/gr.131383.111
109. Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL. 2013. GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics 29:1718–1725. http://dx.doi.org/10.1093/bioinformatics/btt273
110. Phillippy AM, Schatz MC, Pop M. 2008. Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 9:R55. http://dx.doi.org/10.1186/gb-2008-9-3-r55
111. Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. 2013. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform 14:213–224. http://dx.doi.org/10.1093/bib/bbr074
112. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. http://dx.doi.org/10.1093/bioinformatics/btt086
113. Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. 2013. REAPR: a universal tool for genome assembly evaluation. Genome Biol 14:R47. http://dx.doi.org/10.1186/gb-2013-14-5-r47
114. Richardson EJ, Watson M. 2013. The automatic annotation of bacterial genomes. Brief Bioinform 14:1–12. http://dx.doi.org/10.1093/bib/bbs007
115. Soh S, Gordon P, Sensen C. 2012. Genome annotation. Chapman and Hall/CRC, Boca Raton, FL
116. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS. 2005. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 33: W455–W459. http://dx.doi.org/10.1093/nar/gki593
117. Frishman D, Mironov A, Mewes HW, Gelfand M. 1998. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res 26:2941–2947. http://dx.doi.org/10.1093/nar/26.12.2941
118. Badger JH, Olsen GJ. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 16:512–524. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026133
119. Lukashin AV, Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107–1115. http://dx.doi.org/10.1093/nar/26.4.1107
120. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679. http://dx.doi.org/10.1093/bioinformatics/btm009
121. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. http://dx.doi.org/10.1186/1471-2105-11-119
122. Van Domselaar G, Graham MR, Stothard PM. 2014. Prokaryotic genome annotation, p 25–49. In Bishop TO (ed), Bioinformatics and data analysis in microbiology, 1st ed. Horizon Press, Poole, United Kingdom
123. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. http://dx.doi.org/10.1093/nar/25.5.0955
124. Nawrocki EP, Kolbe DL, Eddy SR. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25:1335–1337. http://dx.doi.org/10.1093/bioinformatics/btp157
125. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. http://dx.doi.org/10.1093/nar/gkm160
126. Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium. 2013. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res 41:D584–D589. http://dx.doi.org/10.1093/nar/gks1157
127. Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, van den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R. 2004. The EMBL nucleotide sequence database. Nucleic Acids Res 32:D27–D30. http://dx.doi.org/10.1093/nar/gkh120
128. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. 2001. On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 17:425–428. http://dx.doi.org/10.1016/S0168-9525(01)02372-1
129. Pruitt KD, Tatusova T, Maglott DR. 2005. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33:D501–D504
130. Haft DH, Selengut JD, White O. 2003. The TIGRFAMs database of protein families. Nucleic Acids Res 31:371–373. http://dx.doi.org/10.1093/nar/gkg128
131. Meyer F, Overbeek R, Rodriguez A. 2009. FIGfams: yet another set of protein families. Nucleic Acids Res 37:6643–6654. http://dx.doi.org/10.1093/nar/gkp698
132. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. 2014. Pfam: the protein families database. Nucleic Acids Res 42:D222–D230. http://dx.doi.org/10.1093/nar/gkt1223
133. Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P. 2002. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3:265–274. http://dx.doi.org/10.1093/bib/3.3.265
134. Gattiker A, Gasteiger E, Bairoch A. 2002. ScanProsite: a reference implementation of a PROSITE scanning tool. Appl Bioinformatics 1:107–108
135. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580. http://dx.doi.org/10.1006/jmbi.2000.4315
136. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS. 2010. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608–1615. http://dx.doi.org/10.1093/bioinformatics/btq249
137. Gaasterland T, Sensen CW. 1996. MAGPIE: automated genome interpretation. Trends Genet 12:76–78. http://dx.doi.org/10.1016/0168-9525(96)81406-5
138. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A. 2003. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195. http://dx.doi.org/10.1093/nar/gkg312
139. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Medigue C. 2006. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34: 53–65. http://dx.doi.org/10.1093/nar/gkj406
140. Henson J, Tischler G, Ning Z. 2012. Next-generation sequencing and large genome assemblies. Pharmacogenomics 13:901–915. http://dx.doi.org/10.2217/pgs.12.72
141. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393
142. Stewart AC, Osborne B, Read TD. 2009. DIYA: a bacterial annotation pipeline for any genomics lab. Bioinformatics 25:962–963. http://dx.doi.org/10.1093/bioinformatics/btp097
143. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. http://dx.doi.org/10.1093/bioinformatics/btu153
144. Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. 2013. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet 45: 656–663. http://dx.doi.org/10.1038/ng.2625
145. Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S, Lipsitch M. 2014. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect Dis 14:220–226. http://dx.doi.org/10.1016/S1473-3099(13)70693-5
146. Didelot X, Falush D. 2007. Inference of bacterial microevolution using multilocus sequence data. Genetics 175:1251–1266
147. Didelot X, Wilson DJ. 2015. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 11: e1004041. http://dx.doi.org/10.1371/journal.pcbi.1004041
148. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J, Harris SR. 2015. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using gubbins. Nucleic Acids Res 43:e15. http://dx.doi.org/10.1093/nar/gku1196
149. Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J. 2012. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res 40: e6. http://dx.doi.org/10.1093/nar/gkr928
150. Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE. 2015. ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 16:667. http://dx.doi.org/10.1186/s12864-015-1860-2
151. Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M. 2011. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 12:R30. http://dx.doi.org/10.1186/gb-2011-12-3-r30
152. Dhillon BK, Chiu TA, Laird MR, Langille MG, Brinkman FS. 2013. IslandViewer update: improved genomic island discovery and visualization. Nucleic Acids Res 41:W129–W132. http://dx.doi.org/10.1093/nar/gkt394
153. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Moller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. http://dx.doi.org/10.1128/AAC.02412-14
154. Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. 2014. Singlemolecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med 6:254ra126. http://dx.doi.org/10.1126/scitranslmed.3009845
155. Bose M, Barber RD. 2006. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 6:223–227
156. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352. http://dx.doi.org/10.1093/nar/gkr485
157. Felsenstein J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 266: 418–427. http://dx.doi.org/10.1016/S0076-6879(96)66026-1
158. Gregory TR. 2008. Understanding evolutionary trees. Evol Educ Outreach 1:121–137. http://dx.doi.org/10.1007/s12052-008-0035-x
159. Yang Z, Rannala B. 2012. Molecular phylogenetics: Principles and practice. Nat Rev Genet 13:303–314. http://dx.doi.org/10.1038/nrg3186
160. Baldauf SL. 2003. Phylogeny for the faint of heart: a tutorial. Trends Genet 19:345–351. http://dx.doi.org/10.1016/S0168-9525(03)00112-4
161. Croucher NJ, Harris SR, Grad YH, Hanage WP. 2013. Bacterial genomes in epidemiology—present and future. Philos Trans R Soc Lond B Biol Sci 368:20120202. http://dx.doi.org/10.1098/rstb.2012.0202
162. Chan CX, Ragan MA. 2013. Next-generation phylogenomics. Biol Direct 8:3. http://dx.doi.org/10.1186/1745-6150-8-3
163. Dewey CN. 2012. Whole-genome alignment, p 237–257. In Anisimova M (ed), Evolutionary genomics: statistical and computational methods, vol 1. Humana Press, Totowa, NJ
164. Darling AE, Mau B, Perna NT. 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. http://dx.doi.org/10.1371/journal.pone.0011147
165. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD. 2011. Rapid pneumococcal evolution in response to clinical interventions. Science 331:430–434. http://dx.doi.org/10.1126/science.1198545
166. Treangen TJ, Ondov BD, Koren S, Phillippy AM. 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15:524. http://dx.doi.org/10.1186/s13059-014-0524-x
167. Gadagkar SR, Rosenberg MS, Kumar S. 2005. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol 304:64–74
168. Altenhoff AM, Dessimoz C. 2012. Inferring orthology and paralogy. Methods Mol Biol 855:259–279. http://dx.doi.org/10.1007/978-1-61779-582-4_9
169. Li L, Stoeckert CJ, Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189. http://dx.doi.org/10.1101/gr.1224503
170. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. http://dx.doi.org/10.1038/msb.2011.75
171. Leache AD, Banbury BL, Felsenstein J, de Oca AN, Stamatakis A. 2015. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Syst Biol 64:1032–1047. http://dx.doi.org/10.1093/sysbio/syv053
172. Kuhner MK, Beerli P, Yamato J, Felsenstein J. 2000. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156:439–447
173. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. 2004. Versatile and open software for comparing large genomes. Genome Biol 5:R12. http://dx.doi.org/10.1186/gb-2004-5-2-r12
174. Davis S, Pettengill JB, Luo Y, Payne J, Shpuntoff A, Rand H, Strain E. 2015. CFSAN SNP pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Comput Sci 1:e20. http://dx.doi.org/10.7717/peerj-cs.20
175. Jackson BR, Tarr C, Strain E, Jackson KA, Conrad A, Carleton H, Katz LS, Stroika S, Gould LH, Mody RK, Silk BJ, Beal J, Chen Y, Timme R, Doyle M, Fields A, Wise M, Tillman G, Defibaugh-Chavez S, Kucerova Z, Sabol A, Roache K, Trees E, Simmons M, Wasilenko J, Kubota K, Pouseele H, Klimke W, Besser J, Brown E, Allard M, Gerner-Smidt P. 2016. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin Infect Dis 63:380–386. http://dx.doi.org/10.1093/cid/ciw242
176. Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. 2014. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 31:1077–1088. http://dx.doi.org/10.1093/molbev/msu088
177. Pettengill JB, Luo Y, Davis S, Chen Y, Gonzalez-Escalona N, Ottesen A, Rand H, Allard MW, Strain E. 2014. An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella. PeerJ 2:e620. http://dx.doi.org/10.7717/peerj.620
178. Gardner SN, Hall BG. 2013. When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS One 8:e81760. http://dx.doi.org/10.1371/journal.pone.0081760
179. Gardner SN, Slezak T, Hall BG. 2015. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31:2877–2878. http://dx.doi.org/10.1093/bioinformatics/btv271
180. Schwartz RS, Harkins KM, Stone AC, Cartwright RA. 2015. A composite genome approach to identify phylogenetically informative data from next-generation sequencing.BMC Bioinformatics 16:193. http://dx.doi.org/10.1186/s12859-015-0632-y
181. Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC. 2005. Whole-genome prokaryotic phylogeny. Bioinformatics 21:2329–2335. http://dx.doi.org/10.1093/bioinformatics/bth324
182. Sims GE, Jun SR, Wu GA, Kim SH. 2009. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A 106:2677–2682. http://dx.doi.org/10.1073/pnas.0813249106
183. Sims GE, Kim SH. 2011. Whole-genome phylogeny of Escherichia coli/ Shigella group by feature frequency profiles (FFPs). Proc Natl Acad Sci U S A 108:8329–8334. http://dx.doi.org/10.1073/pnas.1105168108
184. Haubold B, Klotzl F, Pfaffelhuber P. 2015. Andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics 31:1169–1175. http://dx.doi.org/10.1093/bioinformatics/btu815
185. Haubold B. 2014. Alignment-free phylogenetics and population genetics. Brief Bioinform 15:407–418. http://dx.doi.org/10.1093/bib/bbt083
186. Bonham-Carter O, Steele J, Bastola D. 2014. Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Brief Bioinform 15:890–905. http://dx.doi.org/10.1093/bib/bbt052
187. Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. 2013. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 11:728–736. http://dx.doi.org/10.1038/nrmicro3093
188. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC. 2012. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158:1005–1015. http://dx.doi.org/10.1099/mic.0.055459-0
189. Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, Parkhill J, Dingle KE, Bowler IC, Jolley KA, Maiden MC. 2013. Real-time genomic epidemiological evaluation of human campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol 51:2526–2534. http://dx.doi.org/10.1128/JCM.00066-13
190. Bryant D, Moulton V. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255–265
191. Huson DH. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68–73. http://dx.doi.org/10.1093/bioinformatics/14.1.68
192. Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carrico JA. 2012. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics 13:87. http://dx.doi.org/10.1186/1471-2105-13-87
193. Kohl TA, Diel R, Harmsen D, Rothganger J, Walter KM, Merker M, Weniger T, Niemann S. 2014. Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol 52:2479–2486. http://dx.doi.org/10.1128/JCM.00567-14
194. Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MC. 2014. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 15:1138. http://dx.doi.org/10.1186/1471-2164-15-1138
195. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A. 2015. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of listeria monocytogenes. J Clin Microbiol 53: 2869–2876. http://dx.doi.org/10.1128/JCM.01193-15
196. Jolley KA, Maiden MC. 2010. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. http://dx.doi.org/10.1186/1471-2105-11-595
197. Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, Turnsek MA, Guo Y, Wang S, Paxinos EE, Orata F, Gladney LM, Stroika S, Folster JP, Rowe L, Freeman MM, Knox N, Frace M, Boncy J, Graham M, Hammer BK, Boucher Y, Bashir A, Hanage WP, Van Domselaar G, Tarr CL. 2013. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio 4:e00398-13. http://dx.doi.org/10.1128/mBio.00398-13
198. Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS, Engelthaler DM, Bortolaia V, Pearson T, Waters AE, Upadhyay BP, Shrestha SD, Adhikari S, Shakya G, Keim PS, Aarestrup FM. 2011. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. mBio 2:e00157-11. http://dx.doi.org/10.1128/mBio.00157-11
199. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. 2014. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 52:1501–1510. http://dx.doi.org/10.1128/JCM.03617-13
200. Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VP, Nash JH, Taboada EN. 2016. The Salmonella in silico typing resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS One 11:e0147101. http://dx.doi.org/10.1371/journal.pone.0147101
201. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2
202. Cosentino S, Voldby Larsen M, Moller Aarestrup F, Lund O. 2013. PathogenFinder—distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 8:e77302. http://dx.doi.org/10.1371/journal.pone.0077302
203. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348–3357. http://dx.doi.org/10.1128/AAC.00419-13
204. Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. 2014. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6:90. http://dx.doi.org/10.1186/s13073-014-0090-6
205. Lambert D, Carrillo CD, Koziol AG, Manninger P, Blais BW. 2015. GeneSippr: a rapid whole-genome approach for the identification and characterization of foodborne pathogens such as priority Shiga toxigenic Escherichia coli. PLoS One 10:e0122928. http://dx.doi.org/10.1371/journal.pone.0122928
206. Frenay HM, Bunschoten AE, Schouls LM, van Leeuwen WJ, Vandenbroucke-Grauls CM, Verhoef J, Mooi FR. 1996. Molecular typing of methicillin-resistant Staphylococcus aureus on the basis of protein A gene polymorphism. Eur J Clin Microbiol Infect Dis 15:60–64. http://dx.doi.org/10.1007/BF01586186
207. Martin IM, Ison CA, Aanensen DM, Fenton KA, Spratt BG. 2004. Rapid sequence-based identification of gonococcal transmission clusters in a large metropolitan area. J Infect Dis 189:1497–1505. http://dx.doi.org/10.1086/383047
208. Huber CA, Foster NF, Riley TV, Paterson DL. 2013. Challenges for standardization of Clostridium difficile typing methods. J Clin Microbiol 51:2810–2814. http://dx.doi.org/10.1128/JCM.00143-13
209. Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW, Lewis DA, Spratt BG, Unemo M, Persson K, Bjartling C, Brunham R, de Vries HJ, Morre SA, Speksnijder A, Bebear CM, Clerc M, de Barbeyrac B, Parkhill J, Thomson NR. 2012. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 44:413–419. http://dx.doi.org/10.1038/ng.2214
210. Moran-Gilad J, Prior K, Yakunin E, Harrison TG, Underwood A, Lazarovitch T, Valinsky L, Luck C, Krux F, Agmon V, Grotto I, Harmsen D. 2015. Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires’ disease incidents. Euro Surveill 20:21186. http://dx.doi.org/10.2807/1560-7917.ES2015.20.28.21186
211. Frerichs RR, Keim PS, Barrais R, Piarroux R. 2012. Nepalese origin of cholera epidemic in Haiti. Clin Microbiol Infect 18:E158–E163. http://dx.doi.org/10.1111/j.1469-0691.2012.03841.x
212. Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Moller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. 2012. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad SciUSA109:3065–3070. http://dx.doi.org/10.1073/pnas.1121491109
213. Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM, Bajaksouzian S, Benard MF, Jacobs MR, Bonomo RA, Adams MD. 2014. New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. mBio 5:e00963-13. http://dx.doi.org/10.1128/mBio.00963-13
214. Lynch T, Chen L, Peirano G, Gregson DB, Church DL, Conly J, Kreiswirth BN, Pitout JD. 2016. Molecular evolution of a Klebsiella pneumoniae ST278 isolate harboring blaNDM-7 and involved in nosocomial transmission. J Infect Dis http://dx.doi.org/10.1093/infdis/jiw240
215. Cairns MD, Preston MD, Lawley TD, Clark TG, Stabler RA, Wren BW. 2015. Genomic epidemiology of a protracted hospital outbreak caused by a toxin A-negative Clostridium difficile sublineage PCR ribotype 017 strain in London, England. J Clin Microbiol 53:3141–3147. http://dx.doi.org/10.1128/JCM.00648-15
216. Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TE, Crook DW, Donnelly P, Thorson S, Amatya P, Joshi S. 2014. Genome sequencing of an extended series of NDMproducing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community-versus hospitalassociated transmission in an endemic setting. Antimicrob Agents Chemother 58:7347–7357. http://dx.doi.org/10.1128/AAC.03900-14
217. Perna NT, Plunkett G, III, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529–533. http://dx.doi.org/10.1038/35054089
218. Sturdevant GL, Kari L, Gardner DJ, Olivares-Zavaleta N, Randall LB, Whitmire WM, Carlson JH, Goheen MM, Selleck EM, Martens C, Caldwell HD. 2010. Frameshift mutations in a single novel virulence factor alter the in vivo pathogenicity of Chlamydia trachomatis for the female murine genital tract. Infect Immun 78:3660–3668. http://dx.doi.org/10.1128/IAI.00386-10
219. Roetzer A, Diel R, Kohl TA, Ruckert C, Nubel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rusch-Gerdes S, Supply P, Kalinowski J, Niemann S. 2013. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10:e1001387. http://dx.doi.org/10.1371/journal.pmed.1001387
220. Bonner C, Caldwell HD, Carlson JH, Graham MR, Kari L, Sturdevant GL, Tyler S, Zetner A, McClarty G. 2015. Chlamydia trachomatis virulence factor CT135 is stable in vivo but highly polymorphic in vitro. Pathog Dis 73:ftv043. http://dx.doi.org/10.1093/femspd/ftv043
221. Lieberman TD, Michel JB, Aingaran M, Potter-Bynoe G, Roux D, Davis MR, Jr, Skurnik D, Leiby N, LiPuma JJ, Goldberg JB, McAdam AJ, Priebe GP, Kishony R. 2011. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat Genet 43:1275–1280. http://dx.doi.org/10.1038/ng.997
222. Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. 2015. Selective and genetic constraints on pneumococcal serotype switching. PLoS Genet 11: e1005095. http://dx.doi.org/10.1371/journal.pgen.1005095
223. Sanchez-Buso L, Comas I, Jorques G, Gonzalez-Candelas F. 2014. Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates. Nat Genet 46:1205–1211. http://dx.doi.org/10.1038/ng.3114
224. Chen L, Zheng D, Liu B, Yang J, Jin Q. 2016. VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res 44:D694–D697. http://dx.doi.org/10.1093/nar/gkv1239
225. Zhou CE, Smith J, Lam M, Zemla A, Dyer MD, Slezak T. 2007. MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res 35:D391–D394. http://dx.doi.org/10.1093/nar/gkl791
226. Mao C, Abraham D, Wattam AR, Wilson MJ, Shukla M, Yoo HS, Sobral BW. 2015. Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics 31:252–258. http://dx.doi.org/10.1093/bioinformatics/btu631
227. Meric G, Yahara K, Mageiros L, Pascoe B, Maiden MC, Jolley KA, Sheppard SK. 2014. A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic campylobacter. PLoS One 9:e92798. http://dx.doi.org/10.1371/journal.pone.0092798
228. Ren CP, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WM, Pallen MJ. 2004. The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J Bacteriol 186:3547–3560. http://dx.doi.org/10.1128/JB.186.11.3547-3560.2004
229. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O’Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar typhi CT18. Nature 413:848–852. http://dx.doi.org/10.1038/35101607
230. Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Simmonds M, White B, Bason N, Mungall K, Dougan G, Parkhill J. 2009. Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC Genomics 10:36. http://dx.doi.org/10.1186/1471-2164-10-36
231. Ji C, Huang A, Liu W, Pan G, Wang G. 2013. Identification and bioinformatics analysis of pseudogenes from whole genome sequence of Phaeodactylum tricornutum. Chin Sci Bull 58:1010–1017. http://dx.doi.org/10.1007/s11434-012-5174-3
232. Dutilh BE, Backus L, Edwards RA, Wels M, Bayjanov JR, van Hijum SA. 2013. Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics 12:366–380. http://dx.doi.org/10.1093/bfgp/elt008
233. Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA. 2012. PhenoLink—a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics 13:170. http://dx.doi.org/10.1186/1471-2164-13-170
234. Marinier E, Berry C, Weedmark KA, Domaratzki M, Mabon P, Knox NC, Reimer AR, Graham MR, Van Domselaar G. 2015. Neptune: a tool for rapid genomic signature discovery. bioRxiv http://dx.doi.org/10.1101/032227
235. Field N, Cohen T, Struelens MJ, Palm D, Cookson B, Glynn JR, Gallo V, Ramsay M, Sonnenberg P, Maccannell D, Charlett A, Egger M, Green J, Vineis P, Abubakar I. 2014. Strengthening the reporting of molecular epidemiology for infectious diseases (STROME-ID): an extension of the STROBE statement. Lancet Infect Dis 14:341–352. http://dx.doi.org/10.1016/S1473-3099(13)70324-4
236. Aarestrup FM, Koopmans MG. 2016. Sharing data for global infectious disease surveillance and outbreak detection. Trends Microbiol 24:241–245. http://dx.doi.org/10.1016/j.tim.2016.01.009
237. Yozwiak NL, Schaffner SF, Sabeti PC. 2015. Data sharing: make outbreak research open access. Nature 518:477–479. http://dx.doi.org/10.1038/518477a
238. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R, E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium. 2011. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365:718–724. http://dx.doi.org/10.1056/NEJMoa1107643
239. Trifonov V, Khiabanian H, Greenbaum B, Rabadan R. 2009. The origin of the recent swine influenza A(H1N1) virus infecting humans. Euro Surveill 14:19193
240. Reimer AR, Van Domselaar G, Stroika S, Walker M, Kent H, Tarr C, Talkington D, Rowe L, Olsen-Rasmussen M, Frace M, Sammons S, Dahourou GA, Boncy J, Smith AM, Mabon P, Petkau A, Graham M, Gilmour MW, Gerner-Smidt P, V. cholerae Outbreak Genomics Task Force. 2011. Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa. Emerg Infect Dis 17:2113–2121. http://dx.doi.org/10.3201 /eid1711.110794
241. Orata FD, Keim PS, Boucher Y. 2014. The 2010 cholera outbreak in Haiti: how science solved a controversy. PLoS Pathog 10:e1003967. http://dx.doi.org/10.1371/journal.ppat.1003967
242. Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345:1369–1372. http://dx.doi.org/10.1126/science.1259657
243. Vayena E, Salathe M, Madoff LC, Brownstein JS. 2015. Ethical challenges of big data in public health. PLoS Comput Biol 11:e1003904. http://dx.doi.org/10.1371/journal.pcbi.1003904
244. Contreras JL, Reichman JH. 2015. Data access. Sharing by design: data and decentralized commons. Science 350:1312–1314. http://dx.doi.org/10.1126/science.aaa7485
245. Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. 2015. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics 31: 2741–2744. http://dx.doi.org/10.1093/bioinformatics/btv204
246. Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D. 2013. Using Tablet for visual exploration of secondgeneration sequencing data. Brief Bioinform 14:193–202. http://dx.doi.org/10.1093/bib/bbs012
247. Miller CA, Qiao Y, DiSera T, D’Astous B, Marth GT. 2014. Bam.iobio: a web-based, real-time, sequence alignment file inspector. Nat Methods 11:1189. http://dx.doi.org/10.1038/nmeth.3174
248. Oakley T, Alexandrou M, Ngo R, Pankey M, Churchill CK, Chen W, Lopker K. 2014. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics 15:230. http://dx.doi.org/10.1186/1471-2105-15-230
249. Zuo G, Hao B. 2015. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 13:321–331. http://dx.doi.org/10.1016/j.gpb.2015.08.004.