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Volumn 32, Issue 7, 2016, Pages 1088-1090

MetaQUAST: Evaluation of metagenome assemblies

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; GENETIC VARIATION; METAGENOME; METAGENOMICS; SOFTWARE;

EID: 84964414690     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv697     Document Type: Article
Times cited : (420)

References (26)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol. , vol.215 , pp. 403-410
    • Altschul, S.1
  • 2
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich,A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477.
    • (2012) J. Comput. Biol. , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 3
    • 84871396799 scopus 로고    scopus 로고
    • Ray Meta: Scalable de novo metagenome assembly and profiling
    • Boisvert,S. et al. (2012) Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13, R122.
    • (2012) Genome Biol. , vol.13 , pp. R122
    • Boisvert, S.1
  • 4
    • 74049108922 scopus 로고    scopus 로고
    • Blast: Architecture and applications
    • Camacho,C. et al. (2009) Blast: architecture and applications. BMC Bioinformatics, 10, 421.
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 5
    • 84966658505 scopus 로고    scopus 로고
    • Manta: Rapid detection of structural variants and indels for clinical sequencing applications
    • Chen,X. et al. (2015) Manta: rapid detection of structural variants and indels for clinical sequencing applications. Bioinformatics, doi:10. 1093/bioinformatics/ btv710.
    • (2015) Bioinformatics
    • Chen, X.1
  • 6
    • 84874322149 scopus 로고    scopus 로고
    • ALE: A generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
    • Clark,S. et al. (2013) ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics, 29, 435-443.
    • (2013) Bioinformatics , vol.29 , pp. 435-443
    • Clark, S.1
  • 7
    • 84882295406 scopus 로고    scopus 로고
    • De novo likelihood-based measures for comparing genome assemblies
    • Ghodsi,M. et al. (2013) De novo likelihood-based measures for comparing genome assemblies. BMC Res. Notes, 6, 334.
    • (2013) BMC Res. Notes , vol.6 , pp. 334
    • Ghodsi, M.1
  • 8
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: Quality assessment tool for genome assemblies
    • Gurevich,A. et al. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072-1075.
    • (2013) Bioinformatics , vol.29 , pp. 1072-1075
    • Gurevich, A.1
  • 9
    • 84911364768 scopus 로고    scopus 로고
    • Omega: An overlap-graph de novo assembler for metagenomics
    • Haider,B. et al. (2014) Omega: an overlap-graph de novo assembler for metagenomics. Bioinformatics, 30, 2717-2722.
    • (2014) Bioinformatics , vol.30 , pp. 2717-2722
    • Haider, B.1
  • 10
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium et al.
    • Human Microbiome Project Consortium et al. (2012) Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 11
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1
  • 12
    • 84912096454 scopus 로고    scopus 로고
    • LUMPY: A probabilistic framework for structural variant discovery
    • Layer,R. et al. (2014) LUMPY: a probabilistic framework for structural variant discovery. Genome Biol., 15, R84.
    • (2014) Genome Biol. , vol.15 , pp. R84
    • Layer, R.1
  • 13
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li,H. et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 14
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo,R. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 15
    • 84867397631 scopus 로고    scopus 로고
    • Metavelvet: An extension of velvet assembler to de novo metagenome assembly from short sequence reads
    • Namiki,T. et al. (2012) Metavelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res., 40, e155.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e155
    • Namiki, T.1
  • 16
    • 80053366291 scopus 로고    scopus 로고
    • Interactive metagenomic visualization in a Web browser
    • Ondov,B. et al. (2011) Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12, 385.
    • (2011) BMC Bioinformatics , vol.12 , pp. 385
    • Ondov, B.1
  • 17
    • 84929174408 scopus 로고    scopus 로고
    • CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
    • Ounit,R. et al. (2015) CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMCGenomics, 16, 236.
    • (2015) BMCGenomics , vol.16 , pp. 236
    • Ounit, R.1
  • 18
    • 84937040910 scopus 로고    scopus 로고
    • CheckM: Assessing the quality ofmicrobial genomes recovered from isolates, single cells, and metagenomes
    • Parks,D. et al. (2015) CheckM: assessing the quality ofmicrobial genomes recovered from isolates, single cells, and metagenomes. Genome Res., 25, 1043-1055.
    • (2015) Genome Res. , vol.25 , pp. 1043-1055
    • Parks, D.1
  • 19
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng,Y. et al. (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1-8.
    • (2012) Bioinformatics , vol.28 , pp. 1-8
    • Peng, Y.1
  • 20
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin,J. et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1
  • 21
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
    • Quast,C. et al. (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res., 41, D590-D596.
    • (2012) Nucleic Acids Res. , vol.41 , pp. D590-D596
    • Quast, C.1
  • 22
    • 84940907209 scopus 로고    scopus 로고
    • BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
    • Simao,F. et al. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210-3212.
    • (2015) Bioinformatics , vol.31 , pp. 3210-3212
    • Simao, F.1
  • 23
    • 84867645584 scopus 로고    scopus 로고
    • Metagenomic exploration of viruses throughout the Indian Ocean
    • Williamson,S. et al. (2012) Metagenomic exploration of viruses throughout the Indian Ocean. PLoS One, 7, 18.
    • (2012) PLoS One , vol.7 , pp. 18
    • Williamson, S.1
  • 24
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: Ultrafast metagenomic sequence classification using exact alignments
    • Wood,D. E. and Salzberg,S. L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol., 15, R46.
    • (2014) Genome Biol. , vol.15 , pp. R46
    • Wood, D.E.1    Salzberg, S.L.2
  • 25
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Ye,K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1
  • 26
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu,W. et al. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res., 38, e132.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e132
    • Zhu, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.