메뉴 건너뛰기




Volumn 33, Issue 14, 2017, Pages 2082-2088

Pseudoalignment for metagenomic read assignment

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BACTERIAL GENOME; BACTERIUM; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METAGENOMICS; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE;

EID: 85024483948     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btx106     Document Type: Conference Paper
Times cited : (55)

References (32)
  • 1
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 2
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for illumina sequence data
    • Bolger, A.M. et al. (2014) Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics, btu170.
    • (2014) Bioinformatics , pp. btu170
    • Bolger, A.M.1
  • 3
    • 84952009484 scopus 로고    scopus 로고
    • Rapid antibiotic resistance predictions from genome sequence data for S. Aureus and M. Tuberculosis
    • Bradley, P. et al. (2015) Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis. Nat. Commun., 6, 10063.
    • (2015) Nat. Commun. , vol.6 , pp. 10063
    • Bradley, P.1
  • 4
    • 84966283954 scopus 로고    scopus 로고
    • Near-optimal RNA-Seq quantification
    • Bray, N. et al. (2015). Near-optimal RNA-Seq quantification. Nature Biotechnol., 34, 525-527.
    • (2015) Nature Biotechnol. , vol.34 , pp. 525-527
    • Bray, N.1
  • 5
    • 55449131166 scopus 로고    scopus 로고
    • Bioinformatics for whole-genome shotgun sequencing of microbial communities
    • Chen, K. and Pachter, L. (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol., 1, 106-112.
    • (2005) PLoS Comput. Biol. , vol.1 , pp. 106-112
    • Chen, K.1    Pachter, L.2
  • 6
    • 46249103973 scopus 로고    scopus 로고
    • Stem cell transcriptome profiling via massive-scale mRNA sequencing
    • Cloonan, N. et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods, 5, 613-619.
    • (2008) Nat. Methods , vol.5 , pp. 613-619
    • Cloonan, N.1
  • 7
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • Huson, D.H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
    • (2007) Genome Res. , vol.17 , pp. 377-386
    • Huson, D.H.1
  • 8
    • 60849103082 scopus 로고    scopus 로고
    • Methods for comparative metagenomics
    • Huson, D.H. et al. (2009) Methods for comparative metagenomics. BMC Bioinformatics, 10, S12.
    • (2009) BMC Bioinformatics , vol.10 , pp. S12
    • Huson, D.H.1
  • 9
    • 84976887033 scopus 로고    scopus 로고
    • Ensembl genomes 2016: More genomes, more complexity
    • Kersey, P.J. et al. (2016) Ensembl genomes 2016: more genomes, more complexity. Nucleic Acids Res., 44, D574-D580.
    • (2016) Nucleic Acids Res. , vol.44 , pp. D574-D580
    • Kersey, P.J.1
  • 10
    • 84925517557 scopus 로고    scopus 로고
    • Insights from 20 years of bacterial genome sequencing
    • Land, M. et al. (2015) Insights from 20 years of bacterial genome sequencing. Funct. Integr. Genomics, 15, 141-161.
    • (2015) Funct. Integr. Genomics , vol.15 , pp. 141-161
    • Land, M.1
  • 11
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 12
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B. and Dewey, C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 14
    • 84871725334 scopus 로고    scopus 로고
    • GASiC: Metagenomic abundance estimation and diagnostic testing on species level
    • Lindner, M.S. and Renard, B.Y. (2013) GASiC: Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res., 41, e10.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e10
    • Lindner, M.S.1    Renard, B.Y.2
  • 15
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epi-genome in Arabidopsis
    • Lister, R. et al. (2008) Highly integrated single-base resolution maps of the epi-genome in Arabidopsis. Cell, 133, 523-536.
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1
  • 17
    • 84874321000 scopus 로고    scopus 로고
    • Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    • McDavid, A. et al. (2013) Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics, 29, 461-467.
    • (2013) Bioinformatics , vol.29 , pp. 461-467
    • McDavid, A.1
  • 18
    • 84857524013 scopus 로고    scopus 로고
    • Assessment of metagenomic assembly using simulated next generation sequencing data
    • Mende, D.R. et al. (2012) Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE, 7, e31386.
    • (2012) PLoS ONE , vol.7 , pp. e31386
    • Mende, D.R.1
  • 19
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcrip-tomes by RNA-Seq
    • Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcrip-tomes by RNA-Seq. Nat. Methods, 5, 621-628.
    • (2008) Nat. Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1
  • 20
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi, U. et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1
  • 21
    • 79955082292 scopus 로고    scopus 로고
    • Estimation of alternative splicing isoform frequencies from RNA-Seq data
    • Nicolae, M. et al. (2011) Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol., 6, 9.
    • (2011) Algorithms Mol. Biol. , vol.6 , pp. 9
    • Nicolae, M.1
  • 22
    • 84978998700 scopus 로고    scopus 로고
    • Mash: Fast genome and metagenome distance estimation using minhash
    • Ondov, B.D. et al. (2016) Mash: fast genome and metagenome distance estimation using minhash. Genome Biol., 17, 14.
    • (2016) Genome Biol. , vol.17 , pp. 14
    • Ondov, B.D.1
  • 23
    • 84888865593 scopus 로고    scopus 로고
    • Differential abundance analysis for microbial marker-gene surveys
    • Paulson, J.N. et al. (2013) Differential abundance analysis for microbial marker-gene surveys. Nat. Methods, 10, 1200-1202.
    • (2013) Nat. Methods , vol.10 , pp. 1200-1202
    • Paulson, J.N.1
  • 24
    • 84871946825 scopus 로고    scopus 로고
    • Streaming fragment assignment for realtime analysis of sequencing experiments
    • Roberts, A. and Pachter, L. (2013) Streaming fragment assignment for realtime analysis of sequencing experiments. Nat. Methods, 10, 71-73.
    • (2013) Nat. Methods , vol.10 , pp. 71-73
    • Roberts, A.1    Pachter, L.2
  • 25
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson, M.D. et al. (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1
  • 26
    • 33744784298 scopus 로고    scopus 로고
    • An application of statistics to comparative metagenomics
    • Rodriguez-Brito, B. et al. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.
    • (2006) BMC Bioinformatics , vol.7 , pp. 162
    • Rodriguez-Brito, B.1
  • 27
    • 84856496549 scopus 로고    scopus 로고
    • Next generation sequencing and bioinformatic bottlenecks: The current state of metagenomic data analysis
    • Scholz, M.B. et al. (2012) Next generation sequencing and bioinformatic bottlenecks: The current state of metagenomic data analysis. Curr. Opin. Biotechnol., 23, 9-15.
    • (2012) Curr. Opin. Biotechnol. , vol.23 , pp. 9-15
    • Scholz, M.B.1
  • 28
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 29
    • 20244376755 scopus 로고    scopus 로고
    • Comparative metagenomics of microbial communities
    • Tringe, S.G. et al. (2005) Comparative metagenomics of microbial communities. Science, 308, 554-557.
    • (2005) Science , vol.308 , pp. 554-557
    • Tringe, S.G.1
  • 30
    • 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
  • 31
    • 82755170566 scopus 로고    scopus 로고
    • Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads
    • Xia, L.C. et al. (2011) Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads. Plos One, 6, e27992.
    • (2011) Plos One , vol.6 , pp. e27992
    • Xia, L.C.1
  • 32
    • 84875379461 scopus 로고    scopus 로고
    • Shigella strains are not clones of Escherichia coli but sister species in the genus Escherichia
    • Zuo, G. et al. (2013) Shigella strains are not clones of Escherichia coli but sister species in the genus Escherichia. Genomics Proteomics Bioinf., 11, 61-65.
    • (2013) Genomics Proteomics Bioinf. , vol.11 , pp. 61-65
    • Zuo, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.