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Volumn 14, Issue 1, 2013, Pages

MetAMOS: A modular and open source metagenomic assembly and analysis pipeline

Author keywords

[No Author keywords available]

Indexed keywords

ERROR; METAGENOMICS; NEXT GENERATION SEQUENCING; OPEN READING FRAME; PIPELINE; COMPUTER PROGRAM; CONTIG MAPPING; DNA SEQUENCE; PROCEDURES;

EID: 84872152255     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2013-14-1-r2     Document Type: Article
Times cited : (158)

References (100)
  • 2
    • 79952806659 scopus 로고    scopus 로고
    • Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees
    • Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS ONE 2011, 6:12-12.
    • (2011) PLoS ONE , vol.6 , pp. 12-12
    • Wu, D.1    Wu, M.2    Halpern, A.3    Rusch, D.B.4    Yooseph, S.5    Frazier, M.6    Venter, J.C.7    Eisen, J.A.8
  • 4
    • 84855733160 scopus 로고    scopus 로고
    • Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic
    • Varin T, Lovejoy C, Jungblut AD, Vincent WF, Corbeil J: Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic. Appl Environ Microbiol 2011, 78:549-559.
    • (2011) Appl Environ Microbiol , vol.78 , pp. 549-559
    • Varin, T.1    Lovejoy, C.2    Jungblut, A.D.3    Vincent, W.F.4    Corbeil, J.5
  • 14
    • 79955611184 scopus 로고    scopus 로고
    • PhummBL expanded: confidence scores, custom databases, parellelization and more
    • Brady A, Salzberg S: PhummBL expanded: confidence scores, custom databases, parellelization and more. Nat Methods 2011, 8:367.
    • (2011) Nat Methods , vol.8 , pp. 367
    • Brady, A.1    Salzberg, S.2
  • 15
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL: Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6:673-676.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 16
    • 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, 12:8-8.
    • (2011) BMC Bioinformatics , vol.12 , pp. 8-8
    • Clemente, J.C.1    Jansson, J.2    Valiente, G.3
  • 19
    • 79958167222 scopus 로고    scopus 로고
    • Mixture models for analysis of the taxonomic composition of metagenomes
    • Meinicke P, Aßhauer KP, Lingner T: Mixture models for analysis of the taxonomic composition of metagenomes. Bioinformatics 2011, 27:1618-1624.
    • (2011) Bioinformatics , vol.27 , pp. 1618-1624
    • Meinicke, P.1    Aßhauer, K.P.2    Lingner, T.3
  • 21
    • 79251560623 scopus 로고    scopus 로고
    • RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
    • Nalbantoglu OU, Way SF, Hinrichs SH, Sayood K: RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles. BMC Bioinformatics 2011, 12:41-41.
    • (2011) BMC Bioinformatics , vol.12 , pp. 41-41
    • Nalbantoglu, O.U.1    Way, S.F.2    Hinrichs, S.H.3    Sayood, K.4
  • 22
    • 79961139783 scopus 로고    scopus 로고
    • Classifying short genomic fragments from novel lineages using composition and homology
    • Parks DH, MacDonald NJ, Beiko RG: Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics 2011, 12:328-328.
    • (2011) BMC Bioinformatics , vol.12 , pp. 328-328
    • Parks, D.H.1    MacDonald, N.J.2    Beiko, R.G.3
  • 23
    • 84858863014 scopus 로고    scopus 로고
    • Individual genome assembly from complex community short-read metagenomic datasets
    • Luo C, Tsementzi D, Kyrpides NC, Konstantinidis KT: Individual genome assembly from complex community short-read metagenomic datasets. ISME J 2012, 6:898-901.
    • (2012) ISME J , vol.6 , pp. 898-901
    • Luo, C.1    Tsementzi, D.2    Kyrpides, N.C.3    Konstantinidis, K.T.4
  • 24
    • 84867397631 scopus 로고    scopus 로고
    • MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
    • Namiki T, Hachiya T, Tanaka H, Sakakibara Y: MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 2012, 40:e155.
    • (2012) Nucleic Acids Res , vol.40
    • Namiki, T.1    Hachiya, T.2    Tanaka, H.3    Sakakibara, Y.4
  • 26
    • 79952374428 scopus 로고    scopus 로고
    • Genovo: de novo assembly for metagenomes
    • Laserson J, Jojic V, Koller D: Genovo: de novo assembly for metagenomes. J Comput Biol 2011, 18:429-443.
    • (2011) J Comput Biol , vol.18 , pp. 429-443
    • Laserson, J.1    Jojic, V.2    Koller, D.3
  • 29
    • 77958489718 scopus 로고    scopus 로고
    • Ruffus: a lightweight Python library for computational pipelines
    • Goodstadt L: Ruffus: a lightweight Python library for computational pipelines. Bioinformatics 2010, 26:2778-2779.
    • (2010) Bioinformatics , vol.26 , pp. 2778-2779
    • Goodstadt, L.1
  • 30
    • 80054896129 scopus 로고    scopus 로고
    • Bambus 2: Scaffolding Metagenomes
    • Koren S, Treangen TJ, Pop M: Bambus 2: Scaffolding Metagenomes. Bioinformatics 2011, 27:2964-2971.
    • (2011) Bioinformatics , vol.27 , pp. 2964-2971
    • Koren, S.1    Treangen, T.J.2    Pop, M.3
  • 35
    • 56749177261 scopus 로고    scopus 로고
    • Prokaryotic gene prediction using GeneMark and GeneMark.hmm
    • Current Protocols in Bioinformatics John Wiley and Sons, Inc
    • Borodovsky M, Mills R, Besemer J, Lomsadze A: Prokaryotic gene prediction using GeneMark and GeneMark.hmm. Current Protocols in Bioinformatics John Wiley and Sons, Inc; 2002.
    • (2002)
    • Borodovsky, M.1    Mills, R.2    Besemer, J.3    Lomsadze, A.4
  • 36
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: finding the elusive mis-assembly
    • Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 2008, 9:R55-R55.
    • (2008) Genome Biol , vol.9 , pp. R55-R55
    • Phillippy, A.M.1    Schatz, M.C.2    Pop, M.3
  • 42
    • 84869998071 scopus 로고    scopus 로고
    • MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract
    • Ehrlich SD, The MetaHIT Consortium: MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract. Metagenomics Hum Body 2011, 307-316.
    • (2011) Metagenomics Hum Body , pp. 307-316
    • Ehrlich, S.D.1
  • 43
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project C: Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 44
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Human Microbiome Project C: A framework for human microbiome research. Nature 2012, 486:215-221.
    • (2012) Nature , vol.486 , pp. 215-221
  • 45
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley DR: Whole-genome re-sequencing. Curr Opin Genet Dev 2006, 16:545-552.
    • (2006) Curr Opin Genet Dev , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 47
    • 79955724657 scopus 로고    scopus 로고
    • Comparing de novo genome assembly: the long and short of it
    • Narzisi G, Mishra B: Comparing de novo genome assembly: the long and short of it. PLoS ONE 2011, 6:17-17.
    • (2011) PLoS ONE , vol.6 , pp. 17-17
    • Narzisi, G.1    Mishra, B.2
  • 49
    • 79953177468 scopus 로고    scopus 로고
    • Aligning short sequencing reads with Bowtie
    • Chapter 11, Unit 11 17.
    • Langmead B: Aligning short sequencing reads with Bowtie. Curr Protoc Bioinform 2010, Chapter 11, Unit 11 17.
    • (2010) Curr Protoc Bioinform
    • Langmead, B.1
  • 50
    • 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, 9:357-359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 51
    • 85027932848 scopus 로고    scopus 로고
    • State of the art de novo assembly of human genomes from massively parallel sequencing data
    • Li Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data. Hum Genomics 2010, 4:271-277.
    • (2010) Hum Genomics , vol.4 , pp. 271-277
    • Li, Y.1    Hu, Y.2    Bolund, L.3    Wang, J.4
  • 52
    • 79960713932 scopus 로고    scopus 로고
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
    • Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M: Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics 2011, 12:S4.
    • (2011) BMC Genomics , vol.12 , pp. S4
    • Liu, B.1    Gibbons, T.2    Ghodsi, M.3    Treangen, T.4    Pop, M.5
  • 53
    • 84863469252 scopus 로고    scopus 로고
    • Molecular analysis of the glutamate decarboxylase locus in Streptococcus thermophilus ST110
    • Somkuti GA, Renye JA Jr, Steinberg DH: Molecular analysis of the glutamate decarboxylase locus in Streptococcus thermophilus ST110. J Industrial Microbiol Biotechnol 2012, 39:957-963.
    • (2012) J Industrial Microbiol Biotechnol , vol.39 , pp. 957-963
    • Somkuti, G.A.1    Renye, J.A.2    Steinberg, D.H.3
  • 54
    • 36949007183 scopus 로고    scopus 로고
    • Strainer: software for analysis of population variation in community genomic datasets
    • Eppley JM, Tyson GW, Getz WM, Banfield JF: Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics 2007, 8:398.
    • (2007) BMC Bioinformatics , vol.8 , pp. 398
    • Eppley, J.M.1    Tyson, G.W.2    Getz, W.M.3    Banfield, J.F.4
  • 56
    • 33750078701 scopus 로고    scopus 로고
    • Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures
    • Schloss PD, Handelsman J: Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol 2006, 72:6773-6779.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 6773-6779
    • Schloss, P.D.1    Handelsman, J.2
  • 60
    • 84880863425 scopus 로고    scopus 로고
    • Metastats: an improved statistical method for analysis of metagenomic data
    • Paulson JN, Pop M, Corrada Bravo H: Metastats: an improved statistical method for analysis of metagenomic data. Genome Biol 2011, 12(Suppl 1):P17.
    • (2011) Genome Biol , vol.12 , pp. P17
    • Paulson, J.N.1    Pop, M.2    Corrada Bravo, H.3
  • 62
    • 77956967295 scopus 로고    scopus 로고
    • Using the Velvet de novo assembler for short-read sequencing technologies
    • Chapter 11, Unit 11.15.
    • Zerbino DR: Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinform 2010, Chapter 11, Unit 11.15.
    • (2010) Curr Protoc Bioinform
    • Zerbino, D.R.1
  • 63
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 65
    • 84954028896 scopus 로고    scopus 로고
    • PhyloSift
    • PhyloSift. [https://github.com/gjospin/PhyloSift/].
  • 67
    • 84864945803 scopus 로고    scopus 로고
    • Rapid identification of highconfidence taxonomic assignments for metagenomic data
    • MacDonald NJ, Parks DH, Beiko RG: Rapid identification of highconfidence taxonomic assignments for metagenomic data. Nucleic Acids Res 2012, 40:e111.
    • (2012) Nucleic Acids Res , vol.40
    • MacDonald, N.J.1    Parks, D.H.2    Beiko, R.G.3
  • 68
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • Eddy SR: Accelerated Profile HMM Searches. PLoS Comput Biol 2011, 7: e1002195.
    • (2011) PLoS Comput Biol , vol.7
    • Eddy, S.R.1
  • 69
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: predicting genes in short and errorprone reads
    • Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and errorprone reads. Nucleic Acids Res 2010, 38:e191.
    • (2010) Nucleic Acids Res , vol.38
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 70
    • 84855258501 scopus 로고    scopus 로고
    • Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
    • Kelley DR, Liu BB, Delcher AL, Pop M, Salzberg SL: Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res 2012, 40:e9.
    • (2012) Nucleic Acids Res , vol.40
    • Kelley, D.R.1    Liu, B.B.2    Delcher, A.L.3    Pop, M.4    Salzberg, S.L.5
  • 71
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt C: Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-75.
    • (2012) Nucleic Acids Res , vol.40 , pp. D71-75
    • UniProt, C.1
  • 72
    • 84954028897 scopus 로고    scopus 로고
    • FastQC
    • FastQC. [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/].
  • 74
    • 84954028898 scopus 로고    scopus 로고
    • FASTX-Toolkit
    • FASTX-Toolkit. [http://hannonlab.cshl.edu/fastx_toolkit].
  • 76
    • 79953854485 scopus 로고    scopus 로고
    • Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
    • Wetzel J, Kingsford C, Pop M: Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 2011, 12:95.
    • (2011) BMC Bioinformatics , vol.12 , pp. 95
    • Wetzel, J.1    Kingsford, C.2    Pop, M.3
  • 78
    • 84954028899 scopus 로고    scopus 로고
    • MetAMOS
    • MetAMOS. [https://github.com/treangen/MetAMOS].
  • 79
    • 84954028900 scopus 로고    scopus 로고
    • Human Microbiome Project Metagenomes Mock Pilot. [http://www.ncbi. nlm.nih.gov/bioproject/48475].
  • 80
    • 84954028901 scopus 로고    scopus 로고
    • European Nucleotide Archive: Sample ERS006608
    • European Nucleotide Archive: Sample ERS006608. [http://www.ebi.ac.uk/ ena/data/view/ERS006608].
  • 81
    • 84954028902 scopus 로고    scopus 로고
    • Run accession ERR011181 Fastq file 1
    • Run accession ERR011181 Fastq file 1. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011181/ERR011181_1.fastq.gz].
  • 82
    • 84954028903 scopus 로고    scopus 로고
    • Run accession ERR011181 Fastq file 2
    • Run accession ERR011181 Fastq file 2. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011181/ERR011181_2.fastq.gz].
  • 83
    • 84954028904 scopus 로고    scopus 로고
    • European Nucleotide Archive: Sample ERS006507
    • European Nucleotide Archive: Sample ERS006507. [http://www.ebi.ac.uk/ ena/data/view/ERS006507].
  • 84
    • 84954028905 scopus 로고    scopus 로고
    • Run accession ERR011189 Fastq file 1
    • Run accession ERR011189 Fastq file 1. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011189/ERR011189_1.fastq.gz].
  • 85
    • 84954028906 scopus 로고    scopus 로고
    • Run accession ERR011189 Fastq file 2
    • Run accession ERR011189 Fastq file 2. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011189/ERR011189_2.fastq.gz].
  • 86
    • 84954028907 scopus 로고    scopus 로고
    • European Nucleotide Archive: Sample ERS006550
    • European Nucleotide Archive: Sample ERS006550. [http://www.ebi.ac.uk/ ena/data/view/ERS006550].
  • 87
    • 84954028908 scopus 로고    scopus 로고
    • Run accession ERR011209 Fastq file 1
    • Run accession ERR011209 Fastq file 1. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011209/ERR011209_1.fastq.gz].
  • 88
    • 84954028909 scopus 로고    scopus 로고
    • Run accession ERR011209 Fastq file 2
    • Run accession ERR011209 Fastq file 2. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011209/ERR011209_2.fastq.gz].
  • 89
    • 84954028910 scopus 로고    scopus 로고
    • European Nucleotide Archive: Sample ERS006553
    • European Nucleotide Archive: Sample ERS006553. [http://www.ebi.ac.uk/ ena/data/view/ERS006553].
  • 90
    • 84954028911 scopus 로고    scopus 로고
    • Run accession ERR011091 Fastq file 1
    • Run accession ERR011091 Fastq file 1. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011091/ERR011091_1.fastq.gz].
  • 91
    • 84954028912 scopus 로고    scopus 로고
    • Run accession ERR011091 Fastq file 2
    • Run accession ERR011091 Fastq file 2. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011091/ERR011091_2.fastq.gz].
  • 92
    • 84954028913 scopus 로고    scopus 로고
    • European Nucleotide Archive: Sample ERS006585
    • European Nucleotide Archive: Sample ERS006585. [http://www.ebi.ac.uk/ ena/data/view/ERS006585].
  • 93
    • 84954028914 scopus 로고    scopus 로고
    • Run accession ERR011149 Fastq file 1
    • Run accession ERR011149 Fastq file 1. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011149/ERR011149_1.fastq.gz].
  • 94
    • 84954028915 scopus 로고    scopus 로고
    • Run accession ERR011149 Fastq file 2
    • Run accession ERR011149 Fastq file 2. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011149/ERR011149_2.fastq.gz].
  • 95
    • 84954028916 scopus 로고    scopus 로고
    • European Nucleotide Archive: Sample ERS006555
    • European Nucleotide Archive: Sample ERS006555. [http://www.ebi.ac.uk/ ena/data/view/ERS006555].
  • 96
    • 84954028917 scopus 로고    scopus 로고
    • Run accession ERR011264 Fastq file 1
    • Run accession ERR011264 Fastq file 1. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011264/ERR011264_1.fastq.gz].
  • 97
    • 84954028918 scopus 로고    scopus 로고
    • Run accession ERR011264 Fastq file 2
    • Run accession ERR011264 Fastq file 2. [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ ERR011/ERR011264/ERR011264_2.fastq.gz].
  • 98
    • 84954028919 scopus 로고    scopus 로고
    • Perl Artistic License
    • Perl Artistic License. [http://dev.perl.org/licenses/artistic.html].


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