Whole-genome sequencing in bacteriology: state of the art

References

• FleischmannRDAdamsMDWhiteOWhole-genome random sequencing and assembly of Haemophilus influenzae RdScience199526952234965127542800
   PubMed Web of Science ®Google Scholar
• PaganiILioliosKJanssonJThe Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadataNucleic Acids Res201240Database issueD571D57922135293
   PubMed Web of Science ®Google Scholar
• AlsmadiOAlkayalFMoniesDMeyerBFSpecific and complete human genome amplification with improved yield achieved by phi29 DNA polymerase and a novel primer at elevated temperatureBMC Res Notes200924819309528
   PubMedGoogle Scholar
• DarkMJLundgrenAMBarbetAFDetermining the repertoire of immunodominant proteins via whole-genome amplification of intracellular pathogensPLoS One201274e3645622558468
   PubMed Web of Science ®Google Scholar
• WoykeTTigheDMavromatisKOne bacterial cell, one complete genomePLoS One201054e1031420428247
   PubMed Web of Science ®Google Scholar
• LiuLLiYLiSComparison of next-generation sequencing systemsJ Biomed Biotechnol2012201225136422829749
   PubMedGoogle Scholar
• GS FLX+ SystemRoche Corporation 454 Sequencing home page2013Accessed July 26, 2013
   Google Scholar
• QuailMASmithMCouplandPA tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencersBMC Genomics20121334122827831
   PubMed Web of Science ®Google Scholar
• KorenSSchatzMCWalenzBPHybrid error correction and de novo assembly of single-molecule sequencing readsNat Biotechnol201230769370022750884
   PubMed Web of Science ®Google Scholar
• MurrayIAClarkTAMorganRDThe methylomes of six bacteriaNucleic Acids Res20124022114501146223034806
   PubMed Web of Science ®Google Scholar
• CouplandPChandraTQuailMReikWSwerdlowHDirect sequencing of small genomes on the Pacific Biosciences RS without library preparationBiotechniques201253636537223227987
   PubMed Web of Science ®Google Scholar
• GnuBIOGnuBIO home page2013http://gnubio.com/Accessed July 29, 2013
   Google Scholar
• Oxford Nanopore TechnologiesOxford Nanopore Technologies home page2013https://www.nanoporetech.com/Accessed July 29, 2013
   Google Scholar
• SimpsonJTWongKJackmanSDScheinJEJonesSJMBirolƒnABySS: A parallel assembler for short read sequence dataGenome Research20091961117112319251739
   PubMed Web of Science ®Google Scholar
• Celera AssemblerSourceforge: Celera Assembler home page2013http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_PageAccessed July 29, 2013
   Google Scholar
• MillerJRDelcherALKorenSAggressive assembly of pyrosequencing reads with matesBioinformatics200824242818282418952627
   PubMed Web of Science ®Google Scholar
• GillespieJJJoardarVWilliamsKPA Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyleJ Bacteriol2012194237639422056929
   PubMed Web of Science ®Google Scholar
• HernandezDFrancoisPFarinelliLOsterasMSchrenzelJDe novo bacterial genome sequencing: millions of very short reads assembled on a desktop computerGenome Res200818580280918332092
   PubMed Web of Science ®Google Scholar
• ChaissonMJPevznerPAShort read fragment assembly of bacterial genomesGenome Res200818232433018083777
   PubMed Web of Science ®Google Scholar
• Developing Methods for Improving Genome AssemblyThe University of Maryland Genome Assembly Group home page2013http://www.genome.umd.edu/masurca.htmlAccessed August 2, 2013
   Google Scholar
• MagocTPabingerSCanzarSGAGE-B: an evaluation of genome assemblers for bacterial organismsBioinformatics201329141718172523665771
   PubMed Web of Science ®Google Scholar
• ChevreuxBPfistererTDrescherBUsing the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTsGenome Res20041461147115915140833
   PubMed Web of Science ®Google Scholar
• MIRASourceforge MIRA home page2013http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_PageAccessed July 30, 2013
   Google Scholar
• LuoRLiuBXieYSOAPdenovo2: an empirically improved memory-efficient short-read de novo assemblerGigascience2012111823587118
   PubMed Web of Science ®Google Scholar
• DayarianAMichaelTPSenguptaAMSOPRA: Scaffolding algorithm for paired reads via statistical optimizationBMC Bioinformatics20101134520576136
   PubMed Web of Science ®Google Scholar
• ZerbinoDRBirneyEVelvet: algorithms for de novo short read assembly using de Bruijn graphsGenome Res200818582182918349386
   PubMed Web of Science ®Google Scholar
• NagarajanNPopMSequence assembly demystifiedNat Rev Genet201314315716723358380
   PubMed Web of Science ®Google Scholar
• ZerbinoDRMcEwenGKMarguliesEHBirneyEPebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assemblerPLoS One2009412e840720027311
   PubMed Web of Science ®Google Scholar
• MillerJMWhole-genome mapping: a new paradigm in strain-typing technologyJ Clin Microbiol20135141066107023363821
   PubMed Web of Science ®Google Scholar
• Onmus-LeoneFHangJCliffordRJEnhanced de novo assembly of high throughput pyrosequencing data using whole genome mappingPLoS One201384e6176223613926
   PubMed Web of Science ®Google Scholar
• LohseMBolgerAMNagelARobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomicsNucleic Acids Res201240Web Server issueW622W62722684630
   PubMed Web of Science ®Google Scholar
• GrantJRArantesASStothardPComparing thousands of circular genomes using the CGView Comparison ToolBMC Genomics20121320222621371
   PubMed Web of Science ®Google Scholar
• CarverTJRutherfordKMBerrimanMRajandreamMABarrellBGParkhillJACT: the Artemis Comparison ToolBioinformatics200521163422342315976072
   PubMed Web of Science ®Google Scholar
• AbbottJCAanensenDMBentleySDWebACT: an online genome comparison suiteMethods Mol Biol2007395577417993667
   PubMedGoogle Scholar
• GoecksJNekrutenkoATaylorJGalaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciencesGenome Biol2010118R8620738864
   PubMed Web of Science ®Google Scholar
• GoecksJEberhardCTooTNekrutenkoATaylorJWeb-based visual analysis for high-throughput genomicsBMC Genomics20131439723758618
   PubMed Web of Science ®Google Scholar
• TorokMEPeacockSJRapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory – pipe dream or reality?J Antimicrob Chemother201267102307230822729921
   PubMed Web of Science ®Google Scholar
• BertelliCGreubGRapid bacterial genome sequencing: methods and applications in clinical microbiologyClin Microbiol Infect20131998031323601179
   PubMed Web of Science ®Google Scholar
• Seth-SmithHMHarrisSRSkiltonRJWhole-genome sequences of Chlamydia trachomatis directly from clinical samples without cultureGenome Res201323585586623525359
   PubMed Web of Science ®Google Scholar
• ReuterSEllingtonMJCartwrightEJRapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health MicrobiologyJAMA Intern Med2013 (in print)
   Web of Science ®Google Scholar
• SnitkinESZelaznyAMThomasPJTracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencingSci Transl Med20124148148ra116
   PubMed Web of Science ®Google Scholar
• NubelUNachtnebelMFalkenhorstGMRSA transmission on a neonatal intensive care unit: epidemiological and genome-based phylogenetic analysesPLoS One201381e5489823382995
   PubMed Web of Science ®Google Scholar
• EyreDWCuleMLGriffithsDDetection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmissionPLoS Comput Biol201395e100305923658511
   PubMed Web of Science ®Google Scholar
• RaskoDAWorshamPLAbshireTGBacillus anthracis comparative genome analysis in support of the Amerithrax investigationProc Natl Acad Sci U S A2011108125027503221383169
   PubMed Web of Science ®Google Scholar
• FiererNLauberCLZhouNMcDonaldDCostelloEKKnightRForensic identification using skin bacterial communitiesProc Natl Acad Sci U S A2010107146477648120231444
   PubMed Web of Science ®Google Scholar
• RichardsonEJWatsonMThe automatic annotation of bacterial genomesBrief Bioinform201314111222408191
   PubMed Web of Science ®Google Scholar
• JolleyKAMaidenMCAutomated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplarEuro Surveill20131842037923369391
   PubMedGoogle Scholar
• BosKISchuenemannVJGoldingGBA draft genome of Yersinia pestis from victims of the Black DeathNature2011478737050651021993626
   PubMed Web of Science ®Google Scholar
• SchuenemannVJSinghPMendumTAGenome-wide comparison of medieval and modern Mycobacterium lepraeScience2013341614217918323765279
   PubMed Web of Science ®Google Scholar
• De La FuenteCFloresSMoragaMDNA from human ancient bacteria: a novel source of genetic evidence from archaeological dental calculusArchaeometry2013554767778
   Web of Science ®Google Scholar
• PallaFMancusoFPBilleciNMultiple approaches to identify bacteria in archaeological waterlogged woodJournal of Cultural Heritage201314Suppl 3e61e64
   Web of Science ®Google Scholar
• TringeSGvon MeringCKobayashiAComparative metagenomics of microbial communitiesScience2005308572155455715845853
   PubMed Web of Science ®Google Scholar
• Garcia MartinHIvanovaNKuninVMetagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communitiesNat Biotechnol200624101263126916998472
   PubMed Web of Science ®Google Scholar
• TysonGWChapmanJHugenholtzPCommunity structure and metabolism through reconstruction of microbial genomes from the environmentNature20044286978374314961025
   PubMed Web of Science ®Google Scholar
• AlbertsenMHugenholtzPSkarshewskiANielsenKLTysonGWNielsenPHGenome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesNat Biotechnol201331653353823707974
   PubMed Web of Science ®Google Scholar
• SheppardSKDidelotXMericGGenome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in CampylobacterProc Natl Acad Sci U S A201311029119231192723818615
   PubMed Web of Science ®Google Scholar
• QinJLiYCaiZA metagenome-wide association study of gut microbiota in type 2 diabetesNature20124907418556023023125
   PubMed Web of Science ®Google Scholar
• MerhejVGeorgiadesKRaoultDPostgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factorsBrief Funct Genomics201312429130423814139
   PubMed Web of Science ®Google Scholar
• LeeMCMarxCJRepeated, selection-driven genome reduction of accessory genes in experimental populationsPLoS Genet201285e100265122589730
   PubMed Web of Science ®Google Scholar
• PierleSADarkMJDahmenDPalmerGHBraytonKAComparative genomics and transcriptomics of trait-gene associationBMC Genomics20121366923181781
   PubMed Web of Science ®Google Scholar
• BryantJChewapreechaCBentleySDDeveloping insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequencesFuture Microbiol20127111283129623075447
   PubMed Web of Science ®Google Scholar
• FariaJPOverbeekRXiaFRochaMRochaIHenryCSGenomescale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic modelsBrief Bioinform2013
   Web of Science ®Google Scholar