publication . Article . Conference object . 2012

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

an extension of Velvet assembler tode novometagenome assembly from short sequence reads
Toshiaki Namiki; Tsuyoshi Hachiya; Hideaki Tanaka; Yasubumi Sakakibara;
Open Access English
  • Published: 19 Jul 2012 Journal: Nucleic Acids Research, volume 40, issue 20, pages e155-e155 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
Abstract
Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome, resulting in a number of small fragmented scaffolds. The m...
Subjects
free text keywords: Methods Online, Genetics, De Bruijn graph, symbols.namesake, symbols, Connectivity, De Bruijn sequence, Metagenomics, Human gut, Genome, Velvet, biology.organism_classification, biology, Metagenomics: An Alternative Approach to Genomics, Communication, business.industry, business, Computational biology, Contig, DNA sequencing, Conserved sequence
Related Organizations
24 references, page 1 of 2

Venter, JC, Remington, K, Heidelberg, JF, Halpern, AL, Rusch, D, Eisen, JA, Wu, D, Paulsen, I, Nelson, KE, Nelson, W. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004; 304: 66-74 [PubMed]

Kurokawa, K, Itoh, T, Kuwahara, T, Oshima, K, Toh, H, Toyoda, A, Takami, H, Morita, H, Sharma, VK, Srivastava, TP. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res.. 2007; 14: 169-181 [OpenAIRE] [PubMed]

Qin, J, Li, R, Raes, J, Arumugam, M, Burgdorf, KS, Manichanh, C, Nielsen, T, Pons, N, Levenez, F, Yamada, T. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464: 59-65 [OpenAIRE] [PubMed]

Hiatt, JB, Patwardhan, RP, Turner, EH, Lee, C, and Shendure, J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat. Methods. 2010; 7: 119-122 [OpenAIRE] [PubMed]

Chen, K, Pachter, L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol.. 2005; 1: 106-112 [OpenAIRE] [PubMed]

Peng, Y, Leung, HC, Yiu, SM, Chin, FY. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics. 2011; 27: i94-i101 [OpenAIRE] [PubMed]

Laserson, J, Jojic, V, Koller, D. Genovo: de novo assembly for metagenomes. J. Comput. Biol.. 2011; 18: 429-443 [OpenAIRE] [PubMed]

Charuvaka, A, Rangwala, H. Evaluation of short read metagenomic assembly. Proceedings of Bioinformatics and Biomedicine (BIBM), 2010 IEEE International Conference. 2010: 171-178

Ye, Y, Tang, H. An ORFome assembly approach to metagenomics sequences analysis. J. Bioinform. Comput. Biol.. 2009; 7: 455-471 [OpenAIRE] [PubMed]

Saeed, I, Halgamuge, SK. The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments. BMC Genomics. 2009; 10 (Suppl. 3): S10 [OpenAIRE] [PubMed]

Yang, B, Peng, Y, Leung, HC, Yiu, SM, Chen, JC, Chin, FY. Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics. 2010; 11 (Suppl. 2): S5

Wu, YW, Ye, Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol.. 2011; 18: 523-534 [OpenAIRE] [PubMed]

Kunin, V, Copeland, A, Lapidus, A, Mavromatis, K, Hugenholtz, P. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev.. 2008; 72: 557-578 [OpenAIRE] [PubMed]

Nishito, Y, Osana, Y, Hachiya, T, Popendorf, K, Toyoda, A, Fujiyama, A, Itaya, M, Sakakibara, Y. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics. 2010; 11: 243 [OpenAIRE] [PubMed]

Zerbino, DR, Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res.. 2008; 18: 821-829 [OpenAIRE] [PubMed]

24 references, page 1 of 2
Abstract
Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome, resulting in a number of small fragmented scaffolds. The m...
Subjects
free text keywords: Methods Online, Genetics, De Bruijn graph, symbols.namesake, symbols, Connectivity, De Bruijn sequence, Metagenomics, Human gut, Genome, Velvet, biology.organism_classification, biology, Metagenomics: An Alternative Approach to Genomics, Communication, business.industry, business, Computational biology, Contig, DNA sequencing, Conserved sequence
Related Organizations
24 references, page 1 of 2

Venter, JC, Remington, K, Heidelberg, JF, Halpern, AL, Rusch, D, Eisen, JA, Wu, D, Paulsen, I, Nelson, KE, Nelson, W. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004; 304: 66-74 [PubMed]

Kurokawa, K, Itoh, T, Kuwahara, T, Oshima, K, Toh, H, Toyoda, A, Takami, H, Morita, H, Sharma, VK, Srivastava, TP. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res.. 2007; 14: 169-181 [OpenAIRE] [PubMed]

Qin, J, Li, R, Raes, J, Arumugam, M, Burgdorf, KS, Manichanh, C, Nielsen, T, Pons, N, Levenez, F, Yamada, T. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464: 59-65 [OpenAIRE] [PubMed]

Hiatt, JB, Patwardhan, RP, Turner, EH, Lee, C, and Shendure, J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat. Methods. 2010; 7: 119-122 [OpenAIRE] [PubMed]

Chen, K, Pachter, L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol.. 2005; 1: 106-112 [OpenAIRE] [PubMed]

Peng, Y, Leung, HC, Yiu, SM, Chin, FY. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics. 2011; 27: i94-i101 [OpenAIRE] [PubMed]

Laserson, J, Jojic, V, Koller, D. Genovo: de novo assembly for metagenomes. J. Comput. Biol.. 2011; 18: 429-443 [OpenAIRE] [PubMed]

Charuvaka, A, Rangwala, H. Evaluation of short read metagenomic assembly. Proceedings of Bioinformatics and Biomedicine (BIBM), 2010 IEEE International Conference. 2010: 171-178

Ye, Y, Tang, H. An ORFome assembly approach to metagenomics sequences analysis. J. Bioinform. Comput. Biol.. 2009; 7: 455-471 [OpenAIRE] [PubMed]

Saeed, I, Halgamuge, SK. The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments. BMC Genomics. 2009; 10 (Suppl. 3): S10 [OpenAIRE] [PubMed]

Yang, B, Peng, Y, Leung, HC, Yiu, SM, Chen, JC, Chin, FY. Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics. 2010; 11 (Suppl. 2): S5

Wu, YW, Ye, Y. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol.. 2011; 18: 523-534 [OpenAIRE] [PubMed]

Kunin, V, Copeland, A, Lapidus, A, Mavromatis, K, Hugenholtz, P. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev.. 2008; 72: 557-578 [OpenAIRE] [PubMed]

Nishito, Y, Osana, Y, Hachiya, T, Popendorf, K, Toyoda, A, Fujiyama, A, Itaya, M, Sakakibara, Y. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics. 2010; 11: 243 [OpenAIRE] [PubMed]

Zerbino, DR, Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res.. 2008; 18: 821-829 [OpenAIRE] [PubMed]

24 references, page 1 of 2
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publication . Article . Conference object . 2012

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

an extension of Velvet assembler tode novometagenome assembly from short sequence reads
Toshiaki Namiki; Tsuyoshi Hachiya; Hideaki Tanaka; Yasubumi Sakakibara;