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Volumn 16, Issue 1, 2015, Pages

BioMaS: A modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

Author keywords

Bioinformatics; High Throughput Sequencing; Meta barcoding; Metagenomics; Microbiome

Indexed keywords

BACTERIA; BIODIVERSITY; ENVIRONMENTAL MICROBIOLOGY; GENE ENCODING; HTTP; MICROORGANISMS; MOLECULAR BIOLOGY; PIPELINES; THROUGHPUT; WEB SERVICES;

EID: 84938973497     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0595-z     Document Type: Article
Times cited : (48)

References (36)
  • 1
    • 84871808499 scopus 로고    scopus 로고
    • Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
    • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1.
    • (2013) Nucleic Acids Res , vol.41 , Issue.1
    • Klindworth, A.1    Pruesse, E.2    Schweer, T.3    Peplies, J.4    Quast, C.5    Horn, M.6
  • 2
    • 0001781529 scopus 로고    scopus 로고
    • On the primer selection problem in polymerase chain reaction experiments
    • Pearson WR, Robins G, Wrege DE, Zhang TT. On the primer selection problem in polymerase chain reaction experiments. Discrete Appl Math. 1996;71(1-3):231-46.
    • (1996) Discrete Appl Math , vol.71 , Issue.1-3 , pp. 231-246
    • Pearson, W.R.1    Robins, G.2    Wrege, D.E.3    Zhang, T.T.4
  • 3
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • Bazinet AL, Cummings MP. A comparative evaluation of sequence classification programs. BMC Bioinformatics. 2012;13:92.
    • (2012) BMC Bioinformatics , vol.13 , pp. 92
    • Bazinet, A.L.1    Cummings, M.P.2
  • 5
    • 85019194150 scopus 로고    scopus 로고
    • FastQC [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ]
  • 8
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 10
    • 78650933792 scopus 로고    scopus 로고
    • Flexible taxonomic assignment of ambiguous sequencing reads
    • Clemente JC, Jansson J, Valiente G. Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics. 2011;12:8.
    • (2011) BMC Bioinformatics , vol.12 , pp. 8
    • Clemente, J.C.1    Jansson, J.2    Valiente, G.3
  • 12
    • 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, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537-41.
    • (2009) Appl Environ Microbiol , vol.75 , Issue.23 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5    Hollister, E.B.6
  • 14
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    • Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37(Database issue):D141-5.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE , pp. D141-D145
    • Cole, J.R.1    Wang, Q.2    Cardenas, E.3    Fish, J.4    Chai, B.5    Farris, R.J.6
  • 16
    • 84856562355 scopus 로고    scopus 로고
    • The NCBI Taxonomy database
    • Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012;40(Database issue):D136-43.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE , pp. D136-D143
    • Federhen, S.1
  • 18
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: fast length adjustment of short reads to improve genome assemblies
    • Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27(21):2957-63.
    • (2011) Bioinformatics , vol.27 , Issue.21 , pp. 2957-2963
    • Magoc, T.1    Salzberg, S.L.2
  • 19
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460-1.
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1
  • 20
    • 84938980672 scopus 로고    scopus 로고
    • Trim Galore!
    • Trim Galore! [ http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ]
  • 21
    • 84864462144 scopus 로고    scopus 로고
    • METAGENassist: a comprehensive web server for comparative metagenomics
    • Arndt D, Xia J, Liu Y, Zhou Y, Guo AC, Cruz JA, et al. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res. 2012;40(Web Server issue):W88-95.
    • (2012) Nucleic Acids Res , vol.40 , Issue.WEB SERVER ISSUE. , pp. W88-95
    • Arndt, D.1    Xia, J.2    Liu, Y.3    Zhou, Y.4    Guo, A.C.5    Cruz, J.A.6
  • 22
    • 84938993250 scopus 로고    scopus 로고
    • The BioVeL Project: Robust phylogenetic workflows running on the GRID
    • In: EGI Community Forum 2012/EMI Second Technical Conference
    • Donvito G, Vicario S, Notarangelo P, Balech B: The BioVeL Project: Robust phylogenetic workflows running on the GRID. In: EGI Community Forum 2012/EMI Second Technical Conference. 2012.
    • (2012)
    • Donvito, G.1    Vicario, S.2    Notarangelo, P.3    Balech, B.4
  • 25
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J, Galaxy T. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86.
    • (2010) Genome Biol , vol.11 , Issue.8
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    Galaxy, T.4
  • 26
    • 84891813947 scopus 로고    scopus 로고
    • The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks
    • Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2014;42(Database issue):D643-8.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D643-D648
    • Yilmaz, P.1    Parfrey, L.W.2    Yarza, P.3    Gerken, J.4    Pruesse, E.5    Quast, C.6
  • 27
    • 77954748234 scopus 로고    scopus 로고
    • The UNITE database for molecular identification of fungi-recent updates and future perspectives
    • Abarenkov K, Henrik Nilsson R, Larsson KH, Alexander IJ, Eberhardt U, Erland S, et al. The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol. 2010;186(2):281-5.
    • (2010) New Phytol , vol.186 , Issue.2 , pp. 281-285
    • Abarenkov, K.1    Henrik Nilsson, R.2    Larsson, K.H.3    Alexander, I.J.4    Eberhardt, U.5    Erland, S.6
  • 28
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35(Database issue):D61-5.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE , pp. D61-D65
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 30
    • 0033915990 scopus 로고    scopus 로고
    • PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
    • Pesole G, Liuni S, D'Souza M. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics. 2000;16(5):439-50.
    • (2000) Bioinformatics , vol.16 , Issue.5 , pp. 439-450
    • Pesole, G.1    Liuni, S.2    D'Souza, M.3
  • 31
    • 0041620253 scopus 로고    scopus 로고
    • PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences
    • Grillo G, Licciulli F, Liuni S, Sbisa E, Pesole G. PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res. 2003;31(13):3608-12.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3608-3612
    • Grillo, G.1    Licciulli, F.2    Liuni, S.3    Sbisa, E.4    Pesole, G.5
  • 32
    • 77649209317 scopus 로고    scopus 로고
    • Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria
    • Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S, Weber TC, et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 2010;6(1):e1000711.
    • (2010) PLoS Pathog , vol.6 , Issue.1
    • Stecher, B.1    Chaffron, S.2    Kappeli, R.3    Hapfelmeier, S.4    Freedrich, S.5    Weber, T.C.6
  • 34
    • 84857145150 scopus 로고    scopus 로고
    • ART: a next-generation sequencing read simulator
    • Huang WC, Li LP, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28(4):593-4.
    • (2012) Bioinformatics , vol.28 , Issue.4 , pp. 593-594
    • Huang, W.C.1    Li, L.P.2    Myers, J.R.3    Marth, G.T.4
  • 35
    • 77956543003 scopus 로고    scopus 로고
    • Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim
    • Balzer S, Malde K, Lanzen A, Sharma A, Jonassen I. Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics. 2010;26(18):i420-5.
    • (2010) Bioinformatics , vol.26 , Issue.18 , pp. i420-i425
    • Balzer, S.1    Malde, K.2    Lanzen, A.3    Sharma, A.4    Jonassen, I.5
  • 36
    • 84925496272 scopus 로고    scopus 로고
    • The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy
    • (in press).
    • Manzari C, Fosso B, Marzano M, Annese A, Caprioli R, D'Erchia AM, et al. The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy. Biological Invasions 2015, (in press).
    • (2015) Biological Invasions
    • Manzari, C.1    Fosso, B.2    Marzano, M.3    Annese, A.4    Caprioli, R.5    D'Erchia, A.M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.