publication . Article . 2014

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning.

Afiahayati; Sato K.; Sakakibara Y.;
Open Access
  • Published: 27 Nov 2014 Journal: DNA Research, volume 22, pages 69-77 (issn: 1340-2838, eissn: 1756-1663, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet is an extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo when applied to metagenomic sequence reads and is frequently used in this research community. One important open problem for MetaVelvet is its low accuracy and sensitivity in detecting chimer...
Subjects
free text keywords: Genetics, Machine learning, computer.software_genre, computer, Biology, Supervised learning, Metagenomics, Velvet, biology.organism_classification, De Bruijn sequence, Support vector machine, Bioinformatics, Artificial intelligence, business.industry, business, Software, Bottleneck, Assemblers, comic_books.character, comic_books, Full Papers, metagenomic, de novo assembler, short read, microbial community
Related Organizations
21 references, page 1 of 2

Scholz, M.B., Lo, C.C., Chain, P.S.. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol.. 2012; 23: 9-15 [PubMed]

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 [OpenAIRE] [PubMed]

Chen, K., Pachter, L.. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol.. 2005; 1: e24

Lai, B., Ding, R., Li, Y.. A de novo metagenomic assembly program for shotgun dna reads. Bioinformatics. 2012; 28: 1455-62 [PubMed]

Laserson, J., Jojic, V., Koller, D.. Genovo: de novo assembly for metagenomes. J. Comput. Biol.. 2011; 18: 429-43 [OpenAIRE] [PubMed]

Nagarajan, N., Pop, M.. Sequence assembly demystified. Nat. Rev. Genet.. 2013; 14: 157-67 [OpenAIRE] [PubMed]

Peng, Y., Leung, H.C.M., Yiu, S.M.. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics. 2011; 27: i94-101 [OpenAIRE] [PubMed]

Afiahayati, A., Sato, K., Sakakibara, Y.. An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ. 2013; 1: e196 [OpenAIRE] [PubMed]

Peng, Y., Leung, H.C.M., Yiu, S.M.. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012; 28: 1420-8 [OpenAIRE] [PubMed]

Boisvert, S., Raymond, F., Godzaridis, E.. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol.. 2012; 13: r22 [OpenAIRE] [PubMed]

Haider, B., Ahn, T., Bushnell, B.. Omega: an overlap-graph de novo assembler for metagenomics. Bioinformatics. 2014; 30: 2717-2722 [PubMed]

Zerbino, D.R., Birney, E.. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res.. 2008; 18: 821-9 [OpenAIRE] [PubMed]

Zerbino, D.R., McEwen, G.K., Margulies, E.H.. Pebble and Rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE. 2009; 4: e8407 [OpenAIRE] [PubMed]

Luo, R., Liu, B., Xie, Y.. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012; 1: 18 [OpenAIRE] [PubMed]

Myers, E.W., Sutton, G.G., Delcher, A.L.. A whole-genome assembly of Drosophila. Science. 2009; 287: 2196-204 [OpenAIRE] [PubMed]

21 references, page 1 of 2
Abstract
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet is an extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo when applied to metagenomic sequence reads and is frequently used in this research community. One important open problem for MetaVelvet is its low accuracy and sensitivity in detecting chimer...
Subjects
free text keywords: Genetics, Machine learning, computer.software_genre, computer, Biology, Supervised learning, Metagenomics, Velvet, biology.organism_classification, De Bruijn sequence, Support vector machine, Bioinformatics, Artificial intelligence, business.industry, business, Software, Bottleneck, Assemblers, comic_books.character, comic_books, Full Papers, metagenomic, de novo assembler, short read, microbial community
Related Organizations
21 references, page 1 of 2

Scholz, M.B., Lo, C.C., Chain, P.S.. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol.. 2012; 23: 9-15 [PubMed]

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 [OpenAIRE] [PubMed]

Chen, K., Pachter, L.. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol.. 2005; 1: e24

Lai, B., Ding, R., Li, Y.. A de novo metagenomic assembly program for shotgun dna reads. Bioinformatics. 2012; 28: 1455-62 [PubMed]

Laserson, J., Jojic, V., Koller, D.. Genovo: de novo assembly for metagenomes. J. Comput. Biol.. 2011; 18: 429-43 [OpenAIRE] [PubMed]

Nagarajan, N., Pop, M.. Sequence assembly demystified. Nat. Rev. Genet.. 2013; 14: 157-67 [OpenAIRE] [PubMed]

Peng, Y., Leung, H.C.M., Yiu, S.M.. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics. 2011; 27: i94-101 [OpenAIRE] [PubMed]

Afiahayati, A., Sato, K., Sakakibara, Y.. An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ. 2013; 1: e196 [OpenAIRE] [PubMed]

Peng, Y., Leung, H.C.M., Yiu, S.M.. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012; 28: 1420-8 [OpenAIRE] [PubMed]

Boisvert, S., Raymond, F., Godzaridis, E.. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol.. 2012; 13: r22 [OpenAIRE] [PubMed]

Haider, B., Ahn, T., Bushnell, B.. Omega: an overlap-graph de novo assembler for metagenomics. Bioinformatics. 2014; 30: 2717-2722 [PubMed]

Zerbino, D.R., Birney, E.. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Res.. 2008; 18: 821-9 [OpenAIRE] [PubMed]

Zerbino, D.R., McEwen, G.K., Margulies, E.H.. Pebble and Rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE. 2009; 4: e8407 [OpenAIRE] [PubMed]

Luo, R., Liu, B., Xie, Y.. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012; 1: 18 [OpenAIRE] [PubMed]

Myers, E.W., Sutton, G.G., Delcher, A.L.. A whole-genome assembly of Drosophila. Science. 2009; 287: 2196-204 [OpenAIRE] [PubMed]

21 references, page 1 of 2
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publication . Article . 2014

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning.

Afiahayati; Sato K.; Sakakibara Y.;