메뉴 건너뛰기




Volumn 12, Issue 1, 2017, Pages

Comparing and evaluating metagenome assembly tools from a microbiologist's perspective - Not only size matters!

Author keywords

[No Author keywords available]

Indexed keywords

BIOFILM; FOREST SOIL; METAGENOME; METAGENOMICS; MICROBIOLOGY; ORGANISM COMMUNITY; RELIABILITY; SOFTWARE; STATISTICS; BIODIVERSITY; COMPARATIVE STUDY; FOREST; GENETICS; HIGH THROUGHPUT SEQUENCING; MACROCYSTIS; PHYLOGENY; PROCEDURES;

EID: 85009967892     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0169662     Document Type: Review
Times cited : (174)

References (90)
  • 1
    • 19144366982 scopus 로고    scopus 로고
    • The metagenomics of soil
    • PMID: 15931165
    • Daniel R. The metagenomics of soil. Nat Rev Microbiol. 2005; doi: 10.1038/nrmicro1160 PMID: 15931165
    • (2005) Nat Rev Microbiol
    • Daniel, R.1
  • 2
    • 84881138595 scopus 로고    scopus 로고
    • Insights into the phylogeny and coding potential of microbial dark matter
    • PMID: 23851394
    • Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013; doi: 10.1038/nature12352 PMID: 23851394
    • (2013) Nature
    • Rinke, C.1    Schwientek, P.2    Sczyrba, A.3    Ivanova, N.N.4    Anderson, I.J.5    Cheng, J.-F.6
  • 3
    • 84872436756 scopus 로고    scopus 로고
    • Microbial life under extreme energy limitation
    • PMID: 23321532
    • Hoehler TM, Jørgensen BB. Microbial life under extreme energy limitation. Nat Rev Microbiol. 2013; doi: 10.1038/nrmicro2939 PMID: 23321532
    • (2013) Nat Rev Microbiol
    • Hoehler, T.M.1    Jørgensen, B.B.2
  • 4
    • 79953210780 scopus 로고    scopus 로고
    • Metagenomic analyses: Past and future trends
    • PMID: 21169428
    • Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl Env Microbiol. 2011; doi: 10. 1128/AEM.02345-10 PMID: 21169428
    • (2011) Appl Env Microbiol
    • Simon, C.1    Daniel, R.2
  • 5
    • 84906943235 scopus 로고    scopus 로고
    • Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin
    • PMID: 24599070
    • Kaster A-K, Mayer-Blackwell K, Pasarelli B, Spormann AM. Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. ISME J. 2014; doi: 10.1038/ismej. 2014.24 PMID: 24599070
    • (2014) ISME J
    • Kaster, A.-K.1    Mayer-Blackwell, K.2    Pasarelli, B.3    Spormann, A.M.4
  • 6
    • 84936942726 scopus 로고    scopus 로고
    • Unusual biology across a group comprising more than 15% of domain Bacteria
    • PMID: 26083755
    • Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 2015; doi: 10.1038/nature14486 PMID: 26083755
    • (2015) Nature
    • Brown, C.T.1    Hug, L.A.2    Thomas, B.C.3    Sharon, I.4    Castelle, C.J.5    Singh, A.6
  • 9
    • 84941331779 scopus 로고    scopus 로고
    • Back to basics-The influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities
    • PMID: 26182345
    • Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH, Nielsen PH. Back to Basics-The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS One. 2015; doi: 10.1371/journal.pone.0132783 PMID: 26182345
    • (2015) PLoS One
    • Albertsen, M.1    Karst, S.M.2    Ziegler, A.S.3    Kirkegaard, R.H.4    Nielsen, P.H.5
  • 10
    • 84940707204 scopus 로고    scopus 로고
    • A rapid and economical method for efficient DNA extraction from diverse soils suitable for metagenomic applications
    • PMID: 26167854
    • Devi SG, Fathima AA, Radha S, Arunraj R, Curtis WR, Ramya M. A Rapid and Economical Method for Efficient DNA Extraction from Diverse Soils Suitable for Metagenomic Applications. PLoS One. 2015; doi: 10.1371/journal.pone.0132441 PMID: 26167854
    • (2015) PLoS One
    • Devi, S.G.1    Fathima, A.A.2    Radha, S.3    Arunraj, R.4    Curtis, W.R.5    Ramya, M.6
  • 11
    • 83655181356 scopus 로고    scopus 로고
    • Molecular biomass and Meta- Taxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure
    • PMID: 21989224
    • Terrat S, Christen R, Dequiedt S, Lelièvre M, Nowak V, Regnier T, et al. Molecular biomass and Meta- Taxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure. Microb Biotechnol. 2012; doi: 10.1111/j.1751-7915.2011.00307.x PMID: 21989224
    • (2012) Microb Biotechnol
    • Terrat, S.1    Christen, R.2    Dequiedt, S.3    Lelièvre, M.4    Nowak, V.5    Regnier, T.6
  • 12
    • 77956095592 scopus 로고    scopus 로고
    • Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing
    • PMID: 20393571
    • Ghai R, Martin-Cuadrado A-B, Molto AG, Heredia IG, Cabrera R, Martin J, et al. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J. 2010; doi: 10.1038/ismej.2010.44 PMID: 20393571
    • (2010) ISME J
    • Ghai, R.1    Martin-Cuadrado, A.-B.2    Molto, A.G.3    Heredia, I.G.4    Cabrera, R.5    Martin, J.6
  • 13
    • 34548509019 scopus 로고    scopus 로고
    • Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes
    • PMID: 18043661
    • Woebken D, Teeling H, Wecker P, Dumitriu A, Kostadinov I, Delong EF, et al. Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J. 2007; doi: 10.1038/ismej.2007.63 PMID: 18043661
    • (2007) ISME J
    • Woebken, D.1    Teeling, H.2    Wecker, P.3    Dumitriu, A.4    Kostadinov, I.5    Delong, E.F.6
  • 14
    • 84884826911 scopus 로고    scopus 로고
    • The next-generation sequencing revolution and its impact on genomics
    • PMID: 24074859
    • Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell. 2013; doi: 10.1016/j.cell.2013.09.006 PMID: 24074859
    • (2013) Cell
    • Koboldt, D.C.1    Steinberg, K.M.2    Larson, D.E.3    Wilson, R.K.4    Mardis, E.R.5
  • 15
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - The next generation
    • PMID: 19997069
    • Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet. 2010; doi: 10.1038/ nrg2626 PMID: 19997069
    • (2010) Nat Rev Genet
    • Metzker, M.L.1
  • 17
    • 84925636192 scopus 로고    scopus 로고
    • MaxBin: An automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
    • PMID: 25136443
    • Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014; doi: 10.1186/2049-2618-2-26 PMID: 25136443
    • (2014) Microbiome
    • Wu, Y.-W.1    Tang, Y.-H.2    Tringe, S.G.3    Simmons, B.A.4    Singer, S.W.5
  • 18
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • PMID: 23707974
    • Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013; doi: 10.1038/nbt.2579 PMID: 23707974
    • (2013) Nat Biotechnol
    • Albertsen, M.1    Hugenholtz, P.2    Skarshewski, A.3    Nielsen, K.L.4    Tyson, G.W.5    Nielsen, P.H.6
  • 20
    • 84866458820 scopus 로고    scopus 로고
    • MetaCluster 5.0: A two-round binning approach for metagenomic data for low-abundance species in a noisy sample
    • PMID: 22962452
    • Wang Y, Leung HCM, Yiu SM, Chin FYL. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. Bioinformatics. 2012; doi: 10.1093/ bioinformatics/bts397 PMID: 22962452
    • (2012) Bioinformatics
    • Wang, Y.1    Hcm, L.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 21
    • 84943595976 scopus 로고    scopus 로고
    • Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
    • PMID: 26368049
    • Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, et al. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat Biotechnol. 2015; doi: 10.1038/nbt. 3329 PMID: 26368049
    • (2015) Nat Biotechnol
    • Cleary, B.1    Brito, I.L.2    Huang, K.3    Gevers, D.4    Shea, T.5    Young, S.6
  • 22
    • 84893443187 scopus 로고    scopus 로고
    • An extensive evaluation of read trimming effects on Illumina NGS data analysis
    • PMID: 24376861
    • Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One. 2013; doi: 10.1371/journal.pone.0085024 PMID: 24376861
    • (2013) PLoS One
    • Del Fabbro, C.1    Scalabrin, S.2    Morgante, M.3    Giorgi, F.M.4
  • 23
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • PMID: 21278185
    • Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011; doi: 10.1093/bioinformatics/btr026 PMID: 21278185
    • (2011) Bioinformatics
    • Schmieder, R.1    Edwards, R.2
  • 24
    • 84863181401 scopus 로고    scopus 로고
    • Comparison of the two major classes of assembly algorithms: Overlap-layout-consensus and de-bruijn-graph
    • PMID: 22184334
    • Li Z, Chen Y, Mu D, Yuan J, Shi Y, Zhang H, et al. Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph. Brief Funct Genomics. 2012; doi: 10.1093/ bfgp/elr035 PMID: 22184334
    • (2012) Brief Funct Genomics
    • Li, Z.1    Chen, Y.2    Mu, D.3    Yuan, J.4    Shi, Y.5    Zhang, H.6
  • 25
    • 84874194145 scopus 로고    scopus 로고
    • Sequence assembly demystified
    • PMID: 23358380
    • Nagarajan N, Pop M. Sequence assembly demystified. Nat Rev Genet. 2013; doi: 10.1038/nrg3367 PMID: 23358380
    • (2013) Nat Rev Genet
    • Nagarajan, N.1    Pop, M.2
  • 26
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • PMID: 18083777
    • Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res. 2008; doi: 10.1101/gr.7088808 PMID: 18083777
    • (2008) Genome Res
    • Chaisson, M.J.1    Pevzner, P.A.2
  • 27
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • PMID: 11504945
    • Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA. 2001; doi: 10.1073/pnas.171285098 PMID: 11504945
    • (2001) Proc Natl Acad Sci USA
    • Pevzner, P.A.1    Tang, H.2    Waterman, M.S.3
  • 28
    • 77955463346 scopus 로고    scopus 로고
    • Third generation DNA sequencing: Pacific biosciences' single molecule real time technology
    • PMID: 20659677
    • McCarthy A. Third generation DNA sequencing: pacific biosciences' single molecule real time technology. Chem Biol. 2010; doi: 10.1016/j.chembiol.2010.07.004 PMID: 20659677
    • (2010) Chem Biol
    • McCarthy, A.1
  • 29
    • 84907087679 scopus 로고    scopus 로고
    • Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex highly-repetitive transposable elements
    • PMID: 25188499
    • McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, et al. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One. 2014; doi: 10.1371/journal.pone.0106689 PMID: 25188499
    • (2014) PLoS One
    • McCoy, R.C.1    Taylor, R.W.2    Blauwkamp, T.A.3    Kelley, J.L.4    Kertesz, M.5    Pushkarev, D.6
  • 30
    • 84907952658 scopus 로고    scopus 로고
    • A first look at the oxford nanopore MinION sequencer
    • Mikheyev AS, Tin MMY. A first look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour. 2014; doi: 10.1111/1755-0998.12324
    • (2014) Mol Ecol Resour
    • Mikheyev, A.S.1    Tin, M.M.Y.2
  • 31
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • PMID: 20019144
    • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010; doi: 10.1101/gr.097261.109 PMID: 20019144
    • (2010) Genome Res
    • Li, R.1    Zhu, H.2    Ruan, J.3    Qian, W.4    Fang, X.5    Shi, Z.6
  • 32
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • PMID: 23587118
    • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012; doi: 10.1186/2047-217X-1-18 PMID: 23587118
    • (2012) Gigascience
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6
  • 33
    • 84866712746 scopus 로고    scopus 로고
    • Exploiting sparseness in de novo genome assembly
    • PMID: 22537038
    • Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics. 2012; doi: 10.1186/1471-2105-13-S6-S1 PMID: 22537038
    • (2012) BMC Bioinformatics
    • Ye, C.1    Ma, Z.S.2    Cannon, C.H.3    Pop, M.4    Yu, D.W.5
  • 34
    • 79959422558 scopus 로고    scopus 로고
    • Meta-IDBA: A de Novo assembler for metagenomic data
    • PMID: 21685107
    • Peng Y, Leung HCM, Yiu SM, Chin FYL. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics. 2011; doi: 10.1093/bioinformatics/btr216 PMID: 21685107
    • (2011) Bioinformatics
    • Peng, Y.1    Hcm, L.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 35
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • PMID: 22506599
    • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; doi: 10.1089/ cmb.2012.0021 PMID: 22506599
    • (2012) J Comput Biol
    • Bankevich, A.1    Nurk, S.2    Antipov, D.3    Gurevich, A.A.4    Dvorkin, M.5    Kulikov, A.S.6
  • 36
    • 84959190381 scopus 로고    scopus 로고
    • TruSPAdes: Barcode assembly of TruSeq synthetic long reads
    • PMID: 26828418
    • Bankevich A, Pevzner PA. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nat Methods. Nature Research; 2016; 13: 248-250. doi: 10.1038/nmeth.3737 PMID: 26828418
    • (2016) Nat Methods. Nature Research , vol.13 , pp. 248-250
    • Bankevich, A.1    Pevzner, P.A.2
  • 39
    • 84885626275 scopus 로고    scopus 로고
    • Assembling single- cell genomes and mini-metagenomes from chimeric MDA products
    • Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA PMID: 24093227
    • Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, et al. Assembling Single- Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. J Comput Biol. Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA; 2013; 20: 714-737. doi: 10.1089/ cmb.2013.0084 PMID: 24093227
    • (2013) J Comput Biol. Mary Ann Liebert , vol.20 , pp. 714-737
    • Nurk, S.1    Bankevich, A.2    Antipov, D.3    Gurevich, A.A.4    Korobeynikov, A.5    Lapidus, A.6
  • 41
    • 84881309354 scopus 로고    scopus 로고
    • BayesHammer: Bayesian clustering for error correction in single-cell sequencing
    • PMID: 23368723
    • Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics. 2013; doi: 10.1186/1471-2164-14-S1-S7 PMID: 23368723
    • (2013) BMC Genomics
    • Nikolenko, S.I.1    Korobeynikov, A.I.2    Alekseyev, M.A.3
  • 42
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • PMID: 18349386
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; doi: 10.1101/gr.074492.107 PMID: 18349386
    • (2008) Genome Res
    • Zerbino, D.R.1    Birney, E.2
  • 43
    • 84867397631 scopus 로고    scopus 로고
    • MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
    • PMID: 22821567
    • Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012; doi: 10.1093/nar/ gks678 PMID: 22821567
    • (2012) Nucleic Acids Res
    • Namiki, T.1    Hachiya, T.2    Tanaka, H.3    Sakakibara, Y.4
  • 44
    • 84930660464 scopus 로고    scopus 로고
    • MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
    • PMID: 25431440
    • Afiahayati, Sato K Sakakibara Y. MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res. 2014; doi: 10.1093/dnares/dsu041 PMID: 25431440
    • (2014) DNA Res
    • Afiahayati1    Sato, K.2    Sakakibara, Y.3
  • 45
    • 84864446502 scopus 로고    scopus 로고
    • High-speed microbial community profiling
    • PMID: 22688412
    • Haft DH, Tovchigrechko A. High-speed microbial community profiling. Nat Methods. 2012; doi:10.1038/nmeth.2080 PMID: 22688412
    • (2012) Nat Methods
    • Haft, D.H.1    Tovchigrechko, A.2
  • 46
    • 78349238864 scopus 로고    scopus 로고
    • Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    • PMID: 20958248
    • Boisvert S, Laviolette F, Corbeil J. Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies. J Comput Biol. 2010; doi: 10.1089/cmb.2009.0238 PMID: 20958248
    • (2010) J Comput Biol
    • Boisvert, S.1    Laviolette, F.2    Corbeil, J.3
  • 49
    • 27544497879 scopus 로고    scopus 로고
    • The fragment assembly string graph
    • PMID: 16204131
    • Myers EW. The fragment assembly string graph. Bioinformatics. 2005; doi: 10.1093/bioinformatics/ bti1114 PMID: 16204131
    • (2005) Bioinformatics
    • Myers, E.W.1
  • 50
    • 84857838310 scopus 로고    scopus 로고
    • Efficient de novo assembly of large genomes using compressed data structures
    • PMID: 22156294
    • Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012; doi: 10.1101/gr.126953.111 PMID: 22156294
    • (2012) Genome Res
    • Simpson, J.T.1    Durbin, R.2
  • 51
    • 84929626808 scopus 로고    scopus 로고
    • MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
    • PMID: 25609793
    • Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; doi: 10.1093/ bioinformatics/btv033 PMID: 25609793
    • (2015) Bioinformatics
    • Li, D.1    Liu, C.-M.2    Luo, R.3    Sadakane, K.4    Lam, T.-W.5
  • 52
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • PMID: 22495754
    • Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012; doi: 10.1093/bioinformatics/ bts174 PMID: 22495754
    • (2012) Bioinformatics
    • Peng, Y.1    Hcm, L.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 53
    • 84872152255 scopus 로고    scopus 로고
    • MetAMOS: A modular and open source metagenomic assembly and analysis pipeline
    • PMID: 23320958
    • Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, et al. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 2013; doi: 10.1186/gb-2013- 14-1-r2 PMID: 23320958
    • (2013) Genome Biol
    • Treangen, T.J.1    Koren, S.2    Sommer, D.D.3    Liu, B.4    Astrovskaya, I.5    Ondov, B.6
  • 54
    • 84867634981 scopus 로고    scopus 로고
    • MOCAT: A metagenomics assembly and gene prediction toolkit
    • PMID: 23082188
    • Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, et al. MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS One. 2012; doi: 10.1371/journal.pone.0047656 PMID: 23082188
    • (2012) PLoS One
    • Kultima, J.R.1    Sunagawa, S.2    Li, J.3    Chen, W.4    Chen, H.5    Mende, D.R.6
  • 55
    • 84931052513 scopus 로고    scopus 로고
    • De novo meta-assembly of ultra-deep sequencing data
    • PMID: 26072514
    • Mirebrahim H, Close TJ, Lonardi S. De novo meta-assembly of ultra-deep sequencing data. Bioinformatics. 2015; doi: 10.1093/bioinformatics/btv226 PMID: 26072514
    • (2015) Bioinformatics
    • Mirebrahim, H.1    Close, T.J.2    Lonardi, S.3
  • 56
    • 38549139537 scopus 로고    scopus 로고
    • IMG/M: A data management and analysis system for metagenomes
    • Oxford University Press PMID: 17932063
    • Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. Oxford University Press; 2008; doi: 10.1093/nar/gkm869 PMID: 17932063
    • (2008) Nucleic Acids Res
    • Markowitz, V.M.1    Ivanova, N.N.2    Szeto, E.3    Palaniappan, K.4    Chu, K.5    Dalevi, D.6
  • 57
    • 74349110379 scopus 로고    scopus 로고
    • Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes
    • PMID: 20150127
    • Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010; doi: 10.1101/pdb. prot5368 PMID: 20150127
    • (2010) Cold Spring Harb Protoc
    • Glass, E.M.1    Wilkening, J.2    Wilke, A.3    Antonopoulos, D.4    Meyer, F.5
  • 58
    • 84930045803 scopus 로고    scopus 로고
    • Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology
    • PMID: 25644953
    • Fondi M, Liò P. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiol Res. 2015; doi: 10.1016/j.micres.2015.01.003 PMID: 25644953
    • (2015) Microbiol Res
    • Fondi, M.1    Liò, P.2
  • 59
    • 84893221185 scopus 로고    scopus 로고
    • The potential of metagenomic approaches for understanding soil microbial processes
    • Myrold DD, Zeglin LH, Jansson JK. The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes. Soil Sci Soc Am J. 2014
    • (2014) Soil Sci Soc Am J
    • Myrold, D.D.1    Zeglin, L.H.2    Jansson, J.K.3
  • 62
    • 77957917517 scopus 로고    scopus 로고
    • Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborean
    • PMID: 20950420
    • Bengtsson MM, Øvreas L. Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol. 2010; doi: 10.1186/1471-2180-10-261 PMID: 20950420
    • (2010) BMC Microbiol
    • Bengtsson, M.M.1    Øvreas, L.2
  • 63
    • 77954099753 scopus 로고    scopus 로고
    • Seasonal dynamics of bacterial biofilms on the kelp Laminaria hyperborean
    • Bengtsson M, Sjøtun K, Øvreas L. Seasonal dynamics of bacterial biofilms on the kelp Laminaria hyperborea. Aquat Microb Ecol. 2010
    • (2010) Aquat Microb Ecol
    • Bengtsson, M.1    Sjøtun, K.2    Øvreas, L.3
  • 64
    • 84879237060 scopus 로고    scopus 로고
    • The ecology of microbial communities associated with macrocystis pyrifera
    • PMID: 23840715
    • Michelou VK, Caporaso JG, Knight R, Palumbi SR, Wahl M, Bengtsson M, et al. The Ecology of Microbial Communities Associated with Macrocystis pyrifera. PLoS One. 2013; doi: 10.1371/journal.pone. 0067480 PMID: 23840715
    • (2013) PLoS One
    • Michelou, V.K.1    Caporaso, J.G.2    Knight, R.3    Palumbi, S.R.4    Wahl, M.5    Bengtsson, M.6
  • 65
    • 84855937877 scopus 로고    scopus 로고
    • Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
    • PMID: 21776033
    • Baldrian P, Kolařik M,S tursova M, Kopecky J, Valaskova V, Větrovsky T, et al. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J. 2012; doi: 10.1038/ismej.2011.95 PMID: 21776033
    • (2012) ISME J
    • Baldrian, P.1    Kolařik, M.2    Stursova, M.3    Kopecky, J.4    Valaskova, V.5    Větrovsky, T.6
  • 66
    • 84865344067 scopus 로고    scopus 로고
    • Structure, fluctuation and magnitude of a natural grassland soil metagenome
    • PMID: 22297556
    • Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, et al. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. 2012; doi: 10.1038/ismej.2011.197 PMID: 22297556
    • (2012) ISME J
    • Delmont, T.O.1    Prestat, E.2    Keegan, K.P.3    Faubladier, M.4    Robe, P.5    Clark, I.M.6
  • 68
    • 84925021592 scopus 로고    scopus 로고
    • Fast and sensitive protein alignment using DIAMOND
    • PMID: 25402007
    • Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014; doi: 10.1038/nmeth.3176 PMID: 25402007
    • (2014) Nat Methods
    • Buchfink, B.1    Xie, C.2    Huson, D.H.3
  • 69
    • 84884560630 scopus 로고    scopus 로고
    • Microbial community analysis using MEGAN
    • PMID: 24060133
    • Huson DH, Weber N. Microbial community analysis using MEGAN. Methods Enzym. 2013; doi: 10.1016/B978-0-12-407863-5.00021-6 PMID: 24060133
    • (2013) Methods Enzym
    • Huson, D.H.1    Weber, N.2
  • 70
    • 80053366291 scopus 로고    scopus 로고
    • Interactive metagenomic visualization in a Web browser
    • PMID: 21961884
    • Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011; doi: 10.1186/1471-2105-12-385 PMID: 21961884
    • (2011) BMC Bioinformatics
    • Ondov, B.D.1    Bergman, N.H.2    Phillippy, A.M.3
  • 71
  • 72
    • 84931076912 scopus 로고    scopus 로고
    • Reconstructing 16S rRNA genes in metagenomic data
    • PMID: 26072503
    • Yuan C, Lei J, Cole J, Sun Y. Reconstructing 16S rRNA genes in metagenomic data. Bioinformatics. 2015; doi: 10.1093/bioinformatics/btv231 PMID: 26072503
    • (2015) Bioinformatics
    • Yuan, C.1    Lei, J.2    Cole, J.3    Sun, Y.4
  • 73
    • 79956041561 scopus 로고    scopus 로고
    • EMIRGE: Reconstruction of full-length ribosomal genes from microbial community short read sequencing data
    • PMID: 21595876
    • Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF, Pace N, et al. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011; doi: 10.1186/gb-2011-12-5-r44 PMID: 21595876
    • (2011) Genome Biol
    • Miller, C.S.1    Baker, B.J.2    Thomas, B.C.3    Singer, S.W.4    Banfield, J.F.5    Pace, N.6
  • 74
    • 84883464181 scopus 로고    scopus 로고
    • Accurate and universal delineation of prokaryotic species
    • PMID: 23892899
    • Mende DR, Sunagawa S, Zeller G, Bork P. Accurate and universal delineation of prokaryotic species. Nat Methods. 2013; doi: 10.1038/nmeth.2575 PMID: 23892899
    • (2013) Nat Methods
    • Mende, D.R.1    Sunagawa, S.2    Zeller, G.3    Bork, P.4
  • 75
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: Accelerated for clustering the next-generation sequencing data
    • PMID: 23060610
    • Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28: 3150-2. doi: 10.1093/bioinformatics/bts565 PMID: 23060610
    • (2012) Bioinformatics , vol.28 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 76
  • 77
    • 0242668357 scopus 로고    scopus 로고
    • mRNA extraction and reverse transcription-PCR protocol for detection of nifh gene expression by azotobacter vinelandii in soil
    • Burgmann H, Widmer F, SiglerWV, Zeyer J. mRNA Extraction and Reverse Transcription-PCR Protocol for Detection of nifH Gene Expression by Azotobacter vinelandii in Soil. Appl Env Microbiol. 2003
    • (2003) Appl Env Microbiol
    • Burgmann, H.1    Widmer, F.2    Sigler, W.V.3    Zeyer, J.4
  • 78
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • PMID: 24695404
    • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; doi: 10.1093/bioinformatics/btu170 PMID: 24695404
    • (2014) Bioinformatics
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 79
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • PMID: 21903629
    • Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011; doi: 10.1093/bioinformatics/btr507 PMID: 21903629
    • (2011) Bioinformatics
    • Magoč, T.1    Salzberg, S.L.2
  • 80
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • PMID: 20211023
    • Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; doi: 10.1186/1471- 2105-11-119 PMID: 20211023
    • (2010) BMC Bioinformatics , pp. 11-119
    • Hyatt, D.1    Chen, G.-L.2    LoCascio, P.F.3    Land, M.L.4    Larimer, F.W.5    Hauser, L.J.6
  • 82
    • 84856186358 scopus 로고    scopus 로고
    • DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences
    • PMID: 22101057
    • Wright ES, Yilmaz LS, Noguera DR. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol. 2012; doi: 10.1128/AEM.06516-11 PMID: 22101057
    • (2012) Appl Environ Microbiol
    • Wright, E.S.1    Yilmaz, L.S.2    Noguera, D.R.3
  • 83
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • PMID: 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; doi: 10.1093/nar/gkh340 PMID: 15034147
    • (2004) Nucleic Acids Res
    • Edgar, R.C.1
  • 84
    • 84864134721 scopus 로고    scopus 로고
    • SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
    • PMID: 22556368
    • Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012; doi: 10.1093/bioinformatics/bts252 PMID: 22556368
    • (2012) Bioinformatics
    • Pruesse, E.1    Peplies, J.2    Glockner, F.O.3
  • 86
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: Accelerated for clustering the next-generation sequencing data
    • PMID: 23060610
    • Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; doi: 10.1093/bioinformatics/bts565 PMID: 23060610
    • (2012) Bioinformatics
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 87
    • 84906272014 scopus 로고    scopus 로고
    • Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
    • PMID: 25118885
    • Yarza P, Yilmaz P, Pruesse E, Glockner FO, Ludwig W, Schleifer K-H, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014; doi: 10.1038/nrmicro3330 PMID: 25118885
    • (2014) Nat Rev Microbiol
    • Yarza, P.1    Yilmaz, P.2    Pruesse, E.3    Glockner, F.O.4    Ludwig, W.5    Schleifer, K.-H.6
  • 88
    • 0035923604 scopus 로고    scopus 로고
    • Degeneracy and complexity in biological systems
    • PMID: 11698650
    • Edelman GM, Gally JA. Degeneracy and complexity in biological systems. Proc Natl Acad Sci U S A. 2001; doi: 10.1073/pnas.231499798 PMID: 11698650
    • (2001) Proc Natl Acad Sci U S A
    • Edelman, G.M.1    Gally, J.A.2
  • 89
    • 84857145150 scopus 로고    scopus 로고
    • ART: A next-generation sequencing read simulator
    • PMID: 22199392
    • Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012; doi: 10.1093/bioinformatics/btr708 PMID: 22199392
    • (2012) Bioinformatics
    • Huang, W.1    Li, L.2    Myers, J.R.3    Marth, G.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.