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Volumn 14, Issue 2, 2014, Pages 426-434

StreamingTrim 1.0: A Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies

Author keywords

Amplicon libraries; Dynamic trimming; Metagenetics; Next generation sequencing

Indexed keywords

RNA 16S;

EID: 84894243154     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12187     Document Type: Article
Times cited : (33)

References (23)
  • 1
    • 50949131523 scopus 로고    scopus 로고
    • Comparative analysis of human gut microbiota by barcoded pyrosequencing
    • Andersson AF, Lindberg M, Jakobsson H, et al. (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE, 3, e2836.
    • (2008) PLoS ONE , vol.3
    • Andersson, A.F.1    Lindberg, M.2    Jakobsson, H.3
  • 2
    • 84857508990 scopus 로고    scopus 로고
    • Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments
    • Bik HM, Sung W, De Ley P, et al. (2012) Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Molecular Ecology, 21, 1048-1059.
    • (2012) Molecular Ecology , vol.21 , pp. 1048-1059
    • Bik, H.M.1    Sung, W.2    De Ley, P.3
  • 3
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data
    • Cox M, Peterson D, Biggs P (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics, 11, 485.
    • (2010) BMC Bioinformatics , vol.11 , pp. 485
    • Cox, M.1    Peterson, D.2    Biggs, P.3
  • 4
    • 84857560159 scopus 로고    scopus 로고
    • Cosmopolitanism of microbial eukaryotes in the global deep seas
    • Creer S, Sinniger F (2012) Cosmopolitanism of microbial eukaryotes in the global deep seas. Molecular Ecology, 21, 1033-1035.
    • (2012) Molecular Ecology , vol.21 , pp. 1033-1035
    • Creer, S.1    Sinniger, F.2
  • 5
    • 77951929876 scopus 로고    scopus 로고
    • Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
    • Creer S, Fonseca VG, Porazinska DL, et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19, 4-20.
    • (2010) Molecular Ecology , vol.19 , pp. 4-20
    • Creer, S.1    Fonseca, V.G.2    Porazinska, D.L.3
  • 6
    • 79952006773 scopus 로고    scopus 로고
    • Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Haas BJ, Gevers D, Earl AM, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research, 21, 494-504.
    • (2011) Genome Research , vol.21 , pp. 494-504
    • Haas, B.J.1    Gevers, D.2    Earl, A.M.3
  • 8
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology, 12, 1889-1898.
    • (2010) Environmental Microbiology , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 9
    • 79955561412 scopus 로고    scopus 로고
    • JMOTU and taxonerator: turning DNA barcode sequences into annotated operational taxonomic units
    • Jones M, Ghoorah A, Blaxter M (2011) JMOTU and taxonerator: turning DNA barcode sequences into annotated operational taxonomic units. PLoS ONE, 6, e19259.
    • (2011) PLoS ONE , vol.6
    • Jones, M.1    Ghoorah, A.2    Blaxter, M.3
  • 10
    • 84862192626 scopus 로고    scopus 로고
    • Evaluation of 16S rDNA-based community profiling for human microbiome research
    • Jumpstart Consortium Human Microbiome Project Data Generation Working G.
    • Jumpstart Consortium Human Microbiome Project Data Generation Working G (2012) Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS ONE, 7, e39315.
    • (2012) PLoS ONE , vol.7
  • 11
    • 80051955306 scopus 로고    scopus 로고
    • Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments
    • Lecroq B, Lejzerowicz F, Bachar D, et al. (2011) Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proceedings of the National Academy of Sciences of the United States of America, 108, 13177-13182.
    • (2011) Proceedings of the National Academy of Sciences of the United States of America , vol.108 , pp. 13177-13182
    • Lecroq, B.1    Lejzerowicz, F.2    Bachar, D.3
  • 12
    • 84866641975 scopus 로고    scopus 로고
    • PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences
    • Machida RJ, Knowlton N (2012a) PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences. PLoS ONE, 7, e46180.
    • (2012) PLoS ONE , vol.7
    • Machida, R.J.1    Knowlton, N.2
  • 13
    • 84871673447 scopus 로고    scopus 로고
    • Ways to mix multiple PCR amplicons into single 454 run for DNA barcoding
    • Machida RJ, Knowlton N (2012b) Ways to mix multiple PCR amplicons into single 454 run for DNA barcoding. Methods in molecular biology (Clifton, N.J.), 858, 355-361.
    • (2012) Methods in molecular biology (Clifton, N.J.) , vol.858 , pp. 355-361
    • Machida, R.J.1    Knowlton, N.2
  • 14
    • 84859864632 scopus 로고    scopus 로고
    • PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences
    • Machida RJ, Kweskin M, Knowlton N (2012) PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences. PLoS ONE, 7, e35887.
    • (2012) PLoS ONE , vol.7
    • Machida, R.J.1    Kweskin, M.2    Knowlton, N.3
  • 15
    • 77955426485 scopus 로고    scopus 로고
    • Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots
    • Manter DK, Delgado JA, Holm DG, Stong RA (2010) Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microbial Ecology, 60, 157-166.
    • (2010) Microbial Ecology , vol.60 , pp. 157-166
    • Manter, D.K.1    Delgado, J.A.2    Holm, D.G.3    Stong, R.A.4
  • 16
    • 84856468953 scopus 로고    scopus 로고
    • NGS QC Toolkit: a toolkit for quality control of next generation sequencing data
    • Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE, 7, e30619.
    • (2012) PLoS ONE , vol.7
    • Patel, R.K.1    Jain, M.2
  • 17
    • 84861145419 scopus 로고    scopus 로고
    • Exploring the plant-associated bacterial communities in Medicago sativa L
    • Pini F, Frascella A, Santopolo L, et al. (2012) Exploring the plant-associated bacterial communities in Medicago sativa L. BMC Microbiology, 12, 78.
    • (2012) BMC Microbiology , vol.12 , pp. 78
    • Pini, F.1    Frascella, A.2    Santopolo, L.3
  • 18
    • 77954025874 scopus 로고    scopus 로고
    • Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure
    • Porazinska DL, Sung W, Giblin-Davis RM, Thomas WK (2010) Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Molecular Ecology Resources, 10, 666-676.
    • (2010) Molecular Ecology Resources , vol.10 , pp. 666-676
    • Porazinska, D.L.1    Sung, W.2    Giblin-Davis, R.M.3    Thomas, W.K.4
  • 19
    • 84870472070 scopus 로고    scopus 로고
    • BioJava: an open-source framework for bioinformatics in 2012
    • Prlic A, Yates A, Bliven SE, et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693-2695.
    • (2012) Bioinformatics , vol.28 , pp. 2693-2695
    • Prlic, A.1    Yates, A.2    Bliven, S.E.3
  • 20
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T, et al. (2009) Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environment Microbiology, 75, 7537-7541.
    • (2009) Applied and Environment Microbiology , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3
  • 21
    • 80054784996 scopus 로고    scopus 로고
    • ConDeTri - a content dependent read trimmer for illumina data
    • Smeds L, Kunstner A (2011) ConDeTri - a content dependent read trimmer for illumina data. PLoS ONE, 6, e26314.
    • (2011) PLoS ONE , vol.6
    • Smeds, L.1    Kunstner, A.2
  • 23
    • 34548293679 scopus 로고    scopus 로고
    • Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267.
    • (2007) Applied and Environmental Microbiology , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.