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Volumn 16, Issue 1, 2015, Pages

TagDust2: A generic method to extract reads from sequencing data

Author keywords

Next generation sequencing; TagDust

Indexed keywords

MARKOV PROCESSES;

EID: 84926382871     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0454-y     Document Type: Article
Times cited : (48)

References (22)
  • 1
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of dna elements in the human genome
    • Bernstein B, Birney E, Dunham I, Green E, Gunter C, Snyder M. An integrated encyclopedia of dna elements in the human genome. Nature. 2012; 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
    • Bernstein, B.1    Birney, E.2    Dunham, I.3    Green, E.4    Gunter, C.5    Snyder, M.6
  • 3
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the illumina platform
    • Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the illumina platform. Nucleic Acids Res. 2012; 40(1):e3.
    • (2012) Nucleic Acids Res , vol.40 , Issue.1 , pp. e3
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 5
    • 70350669879 scopus 로고    scopus 로고
    • Tagdust-a program to eliminate artifacts from next generation sequencing data
    • Lassmann T, Hayashizaki Y, Daub CO. Tagdust-a program to eliminate artifacts from next generation sequencing data. Bioinformatics. 2009; 25(21):2839-40.
    • (2009) Bioinformatics , vol.25 , Issue.21 , pp. 2839-2840
    • Lassmann, T.1    Hayashizaki, Y.2    Daub, C.O.3
  • 6
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: a flexible trimmer for illumina sequence data
    • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014; 30(15):2114-2120.
    • (2014) Bioinformatics , vol.30 , Issue.15 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 7
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011; 17(1):10.
    • (2011) EMBnet J , vol.17 , Issue.1 , pp. 10
    • Martin, M.1
  • 8
    • 79960698975 scopus 로고    scopus 로고
    • Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
    • Kong Y. Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics. 2011; 98(2):152-3.
    • (2011) Genomics , vol.98 , Issue.2 , pp. 152-153
    • Kong, Y.1
  • 9
    • 84926391905 scopus 로고    scopus 로고
    • 2FASTQ Conversion Software 1.8.4.
    • BCL, 2FASTQ Conversion Software 1.8.4. [ http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html ]
  • 10
    • 84926385603 scopus 로고    scopus 로고
    • fastx-toolkit. [ http://hannonlab.cshl.edu/fastx_toolkit/ ]
  • 11
    • 84873721644 scopus 로고    scopus 로고
    • From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data
    • Camerlengo T, Ozer HG, Onti-Srinivasan R, Yan P, Huang T, Parvin, J, et al. From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data. AMIA Summits Translational Sci Proc. 2012; 2012:1.
    • (2012) AMIA Summits Translational Sci Proc. , vol.2012 , pp. 1
    • Camerlengo, T.1    Ozer, H.G.2    Onti-Srinivasan, R.3    Yan, P.4    Huang, T.5
  • 16
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short dna sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. Mapping short dna sequencing reads and calling variants using mapping quality scores. Genome Res. 2008; 18(11):1851-8.
    • (2008) Genome Res. , vol.18 , Issue.11 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 17
    • 29144483361 scopus 로고    scopus 로고
    • An hmm posterior decoder for sequence feature prediction that includes homology information
    • Koll L, Krogh A, Sonnhammer EL. An hmm posterior decoder for sequence feature prediction that includes homology information. Bioinformatics. 2005; 21(suppl 1):251-257.
    • (2005) Bioinformatics , vol.21 , pp. 251-257
    • Koll, L.1    Krogh, A.2    Sonnhammer, E.L.3
  • 18
    • 0000541351 scopus 로고    scopus 로고
    • A fast bit-vector algorithm for approximate string matching based on dynamic programming
    • Myers G. A fast bit-vector algorithm for approximate string matching based on dynamic programming. J ACM (JACM). 1999; 46(3):395-415.
    • (1999) J ACM (JACM) , vol.46 , Issue.3 , pp. 395-415
    • Myers, G.1
  • 19
    • 84865046802 scopus 로고    scopus 로고
    • Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels
    • Faircloth BC, Glenn TC. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PloS one. 2012; 7(8):42543.
    • (2012) PloS one , vol.7 , Issue.8 , pp. 42543
    • Faircloth, B.C.1    Glenn, T.C.2
  • 20
    • 84890081976 scopus 로고    scopus 로고
    • Aligning sequence reads, clone sequences and assembly contigs with bwa-mem
    • arXiv preprint, arXiv:1303.3997.
    • Li H. Aligning sequence reads, clone sequences and assembly contigs with bwa-mem. arXiv preprint. 2013. arXiv:1303.3997.
    • (2013)
    • Li, H.1
  • 21
    • 79959403670 scopus 로고    scopus 로고
    • Characterization of the single-cell transcriptional landscape by highly multiplex rna-seq
    • Islam S, Kjällquist U, Moliner A, Zajac P, Fan J-B, Lönnerberg P, et al. Characterization of the single-cell transcriptional landscape by highly multiplex rna-seq. Genome Res. 2011; 21(7):1160-7.
    • (2011) Genome Res. , vol.21 , Issue.71 , pp. 1160-1167
    • Islam, S.1    Kjällquist, U.2    Moliner, A.3    Zajac, P.4    Fan, J.-B.5    Lönnerberg, P.6
  • 22
    • 84876996918 scopus 로고    scopus 로고
    • Tophat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Tophat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):36.
    • (2013) Genome Biol. , vol.14 , Issue.4 , pp. 36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.