메뉴 건너뛰기




Volumn 24, Issue 4, 2018, Pages 342-349

A primer on microbial bioinformatics for nonbioinformaticians

Author keywords

Bioinformatics software; Genomic epidemiology; High throughput sequencing; Microbial bioinformatics; Microbial typing

Indexed keywords

AUTHOR; BACTERIAL INFECTION; BIOINFORMATICS; DATA ANALYSIS SOFTWARE; DATA BASE; GENOME; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; MICROBIAL BIOINFORMATICS; NONHUMAN; PERSONAL EXPERIENCE; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; DNA SEQUENCE; MICROBIOLOGICAL EXAMINATION; MOLECULAR EPIDEMIOLOGY; PROCEDURES;

EID: 85041573549     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1016/j.cmi.2017.12.015     Document Type: Review
Times cited : (44)

References (50)
  • 1
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for Illumina sequence data
    • Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (2014), 2114–2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 2
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: ultrafast metagenomic sequence classification using exact alignments
    • R46
    • Wood, D.E., Salzberg, S.L., Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol, 15, 2014 R46.
    • (2014) Genome Biol , vol.15
    • Wood, D.E.1    Salzberg, S.L.2
  • 3
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W.R., Lipman, D.J., Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85 (1988), 2444–2448.
    • (1988) Proc Natl Acad Sci U S A , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 4
    • 84991528460 scopus 로고    scopus 로고
    • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
    • Bradnam, K.R., Fass, J.N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2, 2013, 10.
    • (2013) Gigascience , vol.2 , pp. 10
    • Bradnam, K.R.1    Fass, J.N.2    Alexandrov, A.3    Baranay, P.4    Bechner, M.5    Birol, I.6
  • 6
    • 84908635320 scopus 로고    scopus 로고
    • GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers
    • Jünemann, S., Prior, K., Albersmeier, A., Albaum, S., Kalinowski, J., Goesmann, A., et al. GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS One, 9, 2014, e107014.
    • (2014) PLoS One , vol.9 , pp. e107014
    • Jünemann, S.1    Prior, K.2    Albersmeier, A.3    Albaum, S.4    Kalinowski, J.5    Goesmann, A.6
  • 7
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Gurevich, A., Saveliev, V., Vyahhi, N., Tesler, G., QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29 (2013), 1072–1075.
    • (2013) Bioinformatics , vol.29 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4
  • 8
    • 84870822864 scopus 로고    scopus 로고
    • Tools for mapping high-throughput sequencing data
    • Fonseca, N.A., Rung, J., Brazma, A., Marioni, J.C., Tools for mapping high-throughput sequencing data. Bioinformatics 28 (2012), 3169–3177.
    • (2012) Bioinformatics , vol.28 , pp. 3169-3177
    • Fonseca, N.A.1    Rung, J.2    Brazma, A.3    Marioni, J.C.4
  • 9
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat Methods 9 (2012), 357–359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 10
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li, H., Durbin, R., Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26 (2010), 589–595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 14
    • 84891804612 scopus 로고    scopus 로고
    • The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)
    • Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42 (2014), D206–D214.
    • (2014) Nucleic Acids Res , vol.42 , pp. D206-D214
    • Overbeek, R.1    Olson, R.2    Pusch, G.D.3    Olsen, G.J.4    Davis, J.J.5    Disz, T.6
  • 15
    • 84901417347 scopus 로고    scopus 로고
    • Prokka: rapid prokaryotic genome annotation
    • Seemann, T., Prokka: rapid prokaryotic genome annotation. Bioinformatics 30 (2014), 2068–2069.
    • (2014) Bioinformatics , vol.30 , pp. 2068-2069
    • Seemann, T.1
  • 18
    • 84952802043 scopus 로고    scopus 로고
    • Emergence of the same successful clade among distinct populations of emm89 Streptococcus pyogenes in multiple geographic regions
    • e01780–15
    • Friães, A., Machado, M.P., Pato, C., Carriço, J., Melo-Cristino, J., Ramirez, M., Emergence of the same successful clade among distinct populations of emm89 Streptococcus pyogenes in multiple geographic regions. MBio, 6, 2015 e01780–15.
    • (2015) MBio , vol.6
    • Friães, A.1    Machado, M.P.2    Pato, C.3    Carriço, J.4    Melo-Cristino, J.5    Ramirez, M.6
  • 19
    • 85013485261 scopus 로고    scopus 로고
    • A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era
    • Gordon, M., Yakunin, E., Valinsky, L., Chalifa-Caspi, V., Moran-Gilad, J., ESCMID Study Group for Legionella Infections. A bioinformatics tool for ensuring the backwards compatibility of Legionella pneumophila typing in the genomic era. Clin Microbiol Infect 23 (2017), 306–310.
    • (2017) Clin Microbiol Infect , vol.23 , pp. 306-310
    • Gordon, M.1    Yakunin, E.2    Valinsky, L.3    Chalifa-Caspi, V.4    Moran-Gilad, J.5
  • 21
    • 85021170217 scopus 로고    scopus 로고
    • PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance
    • Van Walle, I., Gerner-Smidt, P., Campos, J., Chinen, I., Concepcion-Acevedo, J., Gilpin, B., et al. PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill, 22, 2017, 30544.
    • (2017) Euro Surveill , vol.22 , pp. 30544
    • Van Walle, I.1    Gerner-Smidt, P.2    Campos, J.3    Chinen, I.4    Concepcion-Acevedo, J.5    Gilpin, B.6
  • 22
    • 85021270816 scopus 로고    scopus 로고
    • A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates
    • Cody, A.J., Bray, J.E., Jolley, K.A., McCarthy, N.D., Maiden, M.C.J., A core genome multi-locus sequence typing scheme for stable, comparative analyses of Campylobacter jejuni and C. coli human disease isolates. J Clin Microbiol 55 (2017), 2086–2097.
    • (2017) J Clin Microbiol , vol.55 , pp. 2086-2097
    • Cody, A.J.1    Bray, J.E.2    Jolley, K.A.3    McCarthy, N.D.4    Maiden, M.C.J.5
  • 23
    • 84925594814 scopus 로고    scopus 로고
    • A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes
    • Bratcher, H.B., Corton, C., Jolley, K.A., Parkhill, J., Maiden, M.C.J., A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics, 15, 2014, 1138.
    • (2014) BMC Genomics , vol.15 , pp. 1138
    • Bratcher, H.B.1    Corton, C.2    Jolley, K.A.3    Parkhill, J.4    Maiden, M.C.J.5
  • 24
    • 85016165991 scopus 로고    scopus 로고
    • Whole genome–based population biology and epidemiological surveillance of Listeria monocytogenes
    • Moura, A., Criscuolo, A., Pouseele, H., Maury, M.M., Leclercq, A., Tarr, C., et al. Whole genome–based population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol, 2, 2016, 16185.
    • (2016) Nat Microbiol , vol.2 , pp. 16185
    • Moura, A.1    Criscuolo, A.2    Pouseele, H.3    Maury, M.M.4    Leclercq, A.5    Tarr, C.6
  • 25
    • 84928036627 scopus 로고    scopus 로고
    • Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy
    • Zhang, J., Halkilahti, J., Hänninen, M.L., Rossi, M., Refinement of whole-genome multilocus sequence typing analysis by addressing gene paralogy. J Clin Microbiol 53 (2015), 1765–1767.
    • (2015) J Clin Microbiol , vol.53 , pp. 1765-1767
    • Zhang, J.1    Halkilahti, J.2    Hänninen, M.L.3    Rossi, M.4
  • 26
    • 85043691870 scopus 로고    scopus 로고
    • chewBBACA: a complete suite for gene-by-gene schema creation and strain identification
    • Silva, M., Machado, M.P., Silva, D.N., Rossi, M., Moran-Gilad, J., Santos, S., et al. chewBBACA: a complete suite for gene-by-gene schema creation and strain identification. bioRxiv, 2018, 10.1101/173146.
    • (2018) bioRxiv
    • Silva, M.1    Machado, M.P.2    Silva, D.N.3    Rossi, M.4    Moran-Gilad, J.5    Santos, S.6
  • 28
    • 84997283916 scopus 로고    scopus 로고
    • Rapid scoring of genes in microbial pan-genome–wide association studies with Scoary
    • Brynildsrud, O., Bohlin, J., Scheffer, L., Eldholm, V., Rapid scoring of genes in microbial pan-genome–wide association studies with Scoary. Genome Biol, 17, 2016, 238.
    • (2016) Genome Biol , vol.17 , pp. 238
    • Brynildsrud, O.1    Bohlin, J.2    Scheffer, L.3    Eldholm, V.4
  • 29
    • 85032474600 scopus 로고    scopus 로고
    • Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations
    • Marinier, E., Zaheer, R., Berry, C., Weedmark, K.A., Domaratzki, M., Mabon, P., et al. Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations. Nucleic Acids Res, 45, 2017, e159.
    • (2017) Nucleic Acids Res , vol.45 , pp. e159
    • Marinier, E.1    Zaheer, R.2    Berry, C.3    Weedmark, K.A.4    Domaratzki, M.5    Mabon, P.6
  • 31
    • 84933069206 scopus 로고    scopus 로고
    • Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
    • Croucher, N.J., Page, A.J., Connor, T.R., Delaney, A.J., Keane, J.A., Bentley, S.D., et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res, 43, 2015, e15.
    • (2015) Nucleic Acids Res , vol.43 , pp. e15
    • Croucher, N.J.1    Page, A.J.2    Connor, T.R.3    Delaney, A.J.4    Keane, J.A.5    Bentley, S.D.6
  • 32
    • 84924405242 scopus 로고    scopus 로고
    • ClonalFrameML: efficient inference of recombination in whole bacterial genomes
    • Didelot, X., Wilson, D.J., ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol, 11, 2015, e1004041.
    • (2015) PLoS Comput Biol , vol.11 , pp. e1004041
    • Didelot, X.1    Wilson, D.J.2
  • 33
    • 85030710749 scopus 로고    scopus 로고
    • SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
    • Petkau, A., Mabon, P., Sieffert, C., Knox, N.C., Cabral, J., Iskander, M., et al. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom, 3, 2017, e000116.
    • (2017) Microb Genom , vol.3 , pp. e000116
    • Petkau, A.1    Mabon, P.2    Sieffert, C.3    Knox, N.C.4    Cabral, J.5    Iskander, M.6
  • 34
    • 85016616312 scopus 로고    scopus 로고
    • A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens
    • Katz, L.S., Griswold, T., Williams-Newkirk, A.J., Wagner, D., Petkau, A., Sieffert, C., et al. A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens. Front Microbiol, 8, 2017, 375.
    • (2017) Front Microbiol , vol.8 , pp. 375
    • Katz, L.S.1    Griswold, T.2    Williams-Newkirk, A.J.3    Wagner, D.4    Petkau, A.5    Sieffert, C.6
  • 35
    • 84973504216 scopus 로고    scopus 로고
    • CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data
    • Davis, S., Pettengill, J.B., Luo, Y., Payne, J., Shpuntoff, A., Rand, H., et al. CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Comput Sci, 1, 2015, e20.
    • (2015) PeerJ Comput Sci , vol.1 , pp. e20
    • Davis, S.1    Pettengill, J.B.2    Luo, Y.3    Payne, J.4    Shpuntoff, A.5    Rand, H.6
  • 36
    • 85022158148 scopus 로고    scopus 로고
    • MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets
    • Kumar, S., Stecher, G., Tamura, K., MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33 (2016), 1870–1874.
    • (2016) Mol Biol Evol , vol.33 , pp. 1870-1874
    • Kumar, S.1    Stecher, G.2    Tamura, K.3
  • 37
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2—approximately maximum-likelihood trees for large alignments
    • Price, M.N., Dehal, P.S., Arkin, A.P., FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One, 5, 2010, e9490.
    • (2010) PLoS One , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 38
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis, A., RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30 (2014), 1312–1313.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 39
    • 84928040686 scopus 로고    scopus 로고
    • SRST2: rapid genomic surveillance for public health and hospital microbiology labs
    • Inouye, M., Dashnow, H., Raven, L.A., Schultz, M.B., Pope, B.J., Tomita, T., et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med, 6, 2014, 90.
    • (2014) Genome Med , vol.6 , pp. 90
    • Inouye, M.1    Dashnow, H.2    Raven, L.A.3    Schultz, M.B.4    Pope, B.J.5    Tomita, T.6
  • 40
    • 84996946612 scopus 로고    scopus 로고
    • Epidemiological surveillance and typing methods to track antibiotic resistant strains using high throughput sequencing
    • Machado, M.P., Ribeiro-Gonçalves, B., Silva, M., Ramirez, M., Carriço, J.A., Epidemiological surveillance and typing methods to track antibiotic resistant strains using high throughput sequencing. Methods Mol Biol 1520 (2017), 331–356.
    • (2017) Methods Mol Biol , vol.1520 , pp. 331-356
    • Machado, M.P.1    Ribeiro-Gonçalves, B.2    Silva, M.3    Ramirez, M.4    Carriço, J.A.5
  • 41
    • 85020736816 scopus 로고    scopus 로고
    • Comparative analyses of selection operating on nontranslated intergenic regions of diverse bacterial species
    • Thorpe, H.A., Bayliss, S.C., Hurst, L.D., Feil, E.J., Comparative analyses of selection operating on nontranslated intergenic regions of diverse bacterial species. Genetics 206 (2017), 363–376.
    • (2017) Genetics , vol.206 , pp. 363-376
    • Thorpe, H.A.1    Bayliss, S.C.2    Hurst, L.D.3    Feil, E.J.4
  • 42
    • 85011113621 scopus 로고    scopus 로고
    • Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
    • Argimón, S., Abudahab, K., Goater, R.J., Fedosejev, A., Bhai, J., Glasner, C., et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom, 2, 2016, e000093.
    • (2016) Microb Genom , vol.2 , pp. e000093
    • Argimón, S.1    Abudahab, K.2    Goater, R.J.3    Fedosejev, A.4    Bhai, J.5    Glasner, C.6
  • 43
    • 84880764850 scopus 로고    scopus 로고
    • GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework
    • Parks, D.H., Mankowski, T., Zangooei, S., Porter, M.S., Armanini, D.G., Baird, D.J., et al. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One, 8, 2013, e69885.
    • (2013) PLoS One , vol.8 , pp. e69885
    • Parks, D.H.1    Mankowski, T.2    Zangooei, S.3    Porter, M.S.4    Armanini, D.G.5    Baird, D.J.6
  • 44
    • 85014853204 scopus 로고    scopus 로고
    • PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
    • Nascimento, M., Sousa, A., Ramirez, M., Francisco, A.P., Carriço, J.A., Vaz, C., et al. PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics 33 (2017), 128–129.
    • (2017) Bioinformatics , vol.33 , pp. 128-129
    • Nascimento, M.1    Sousa, A.2    Ramirez, M.3    Francisco, A.P.4    Carriço, J.A.5    Vaz, C.6
  • 45
    • 85014321086 scopus 로고    scopus 로고
    • PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees
    • Ribeiro-Gonçalves, B., Francisco, A.P., Vaz, C., Ramirez, M., Carriço, J.A., PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. Nucleic Acids Res 44 (2016), W246–W251.
    • (2016) Nucleic Acids Res , vol.44 , pp. W246-W251
    • Ribeiro-Gonçalves, B.1    Francisco, A.P.2    Vaz, C.3    Ramirez, M.4    Carriço, J.A.5
  • 46
    • 85016156501 scopus 로고    scopus 로고
    • MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes
    • Vallenet, D., Calteau, A., Cruveiller S, Gachet, M., Lajus, A., Josso, A., et al. MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. Nucleic Acids Res 45 (2017), D517–D528.
    • (2017) Nucleic Acids Res , vol.45 , pp. D517-D528
    • Vallenet, D.1    Calteau, A.2    Cruveiller, S.3    Gachet, M.4    Lajus, A.5    Josso, A.6
  • 48
    • 85016050964 scopus 로고    scopus 로고
    • CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
    • Jia, B., Raphenya, A.R., Alcock, B., Waglechner, N., Guo, P., et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45 (2017), D566–D573.
    • (2017) Nucleic Acids Res , vol.45 , pp. D566-D573
    • Jia, B.1    Raphenya, A.R.2    Alcock, B.3    Waglechner, N.4    Guo, P.5
  • 49
    • 84976869393 scopus 로고    scopus 로고
    • VFDB 2016: Hierarchical and refined dataset for big data analysis—10 years on
    • D694–7
    • Chen, L., Zheng, D., Liu, B., Yang, J., Jin, Q., VFDB 2016: Hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res, 44, 2016 D694–7.
    • (2016) Nucleic Acids Res , vol.44
    • Chen, L.1    Zheng, D.2    Liu, B.3    Yang, J.4    Jin, Q.5
  • 50
    • 84862100340 scopus 로고    scopus 로고
    • ICEberg: a web-based resource for integrative and conjugative elements found in bacteria
    • Bi, D., Xu, Z., Harrison, E.M., Tai C, Wei, Y., He, X., et al. ICEberg: a web-based resource for integrative and conjugative elements found in bacteria. Nucleic Acids Res 40 (2012), D621–D626.
    • (2012) Nucleic Acids Res , vol.40 , pp. D621-D626
    • Bi, D.1    Xu, Z.2    Harrison, E.M.3    Tai, C.4    Wei, Y.5    He, X.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.