publication . Other literature type . Article . 2017

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

Francesca Giordano; Louise Aigrain; Michael A Quail; Paul Coupland; James K Bonfield; Robert M Davies; German Tischler; David K Jackson; Thomas M Keane; Jing Li; ...
  • Published: 21 Jun 2017
  • Publisher: Springer Science and Business Media LLC
Abstract
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies usin...
Subjects
free text keywords: Article, Computational biology, Yeast genome, Genome, Bacterial genome size, Nanopore sequencing, Pacific biosciences, Computer science, Contig, Hybrid genome assembly, Genetics, Minion
27 references, page 1 of 2

Sanger, F, Nicklen, S, Coulson, A. Dna sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci.. 1977; 74 (12): 5463-5467 [OpenAIRE] [PubMed] [DOI]

Goodwin, S, McPherson, JD, McCombie, WR. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet.. 2016; 17: 333-351 [OpenAIRE] [PubMed] [DOI]

3.Liu, L. et al. Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology 2012, Article ID 251364 (2012).

4.Glenn, T. 2016 NGS field guide: Overview. http://www.molecularecologist.com/next-gen-fieldguide-2016 (2016).

Quick, J. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016; 530: 228-232 [OpenAIRE] [PubMed] [DOI]

6.Hoenen, T. et al. Nanopore sequencing as a rapidly deployable ebola outbreak response tool. Emerg Infect Dis 22 (2015).

7.Faria, N. R. Zibra project: real-time sequencing of zika virus in brazil. https://nanoporetech.com/publications/zibra-project-real-time-sequencing-zika-virus-brazil (2016).

8.Parker, J., Helmstetter, A. J., Devey, D. S. & Papadopulos, A. S. T. Field-based species identification in eukaryotes using single molecule, real-time sequencing. bioRxiv (Cold Spring Harbor Labs Journals), doi:10.1101/107656 (2017).

Judge, K, Harris, SR, Reuter, S, Parkhill, J, Peacock, SJ. Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J. Antimicrob. Chemother.. 2015; 70: 2775-2778 [OpenAIRE] [PubMed] [DOI]

Greninger, AL. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Medicine. 2015; 7: 99 [OpenAIRE] [PubMed] [DOI]

11.Schmidt, K. et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. Journal of Antimicrobial Chemotherapy, doi:10.1093/jac/dkw397 (2016).

12.Istace, B. et al. de novo assembly and population genomic survey of natural yeast isolates with the oxford nanopore minion sequencer. bioRxiv (Cold Spring Harbor Labs Journals), doi:10.1101/066613 (2016).

Koren, S. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. 2012; 30: 693-700 [OpenAIRE] [PubMed] [DOI]

14.Koren, S., Walenz, B., Berlin, K., Miller, J. & AM, P. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, doi:10.1101/gr.215087.116 (2017).

15.Chin, C. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods, doi:10.1038/nmeth.4035 (2016).

27 references, page 1 of 2
Abstract
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies usin...
Subjects
free text keywords: Article, Computational biology, Yeast genome, Genome, Bacterial genome size, Nanopore sequencing, Pacific biosciences, Computer science, Contig, Hybrid genome assembly, Genetics, Minion
27 references, page 1 of 2

Sanger, F, Nicklen, S, Coulson, A. Dna sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci.. 1977; 74 (12): 5463-5467 [OpenAIRE] [PubMed] [DOI]

Goodwin, S, McPherson, JD, McCombie, WR. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet.. 2016; 17: 333-351 [OpenAIRE] [PubMed] [DOI]

3.Liu, L. et al. Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology 2012, Article ID 251364 (2012).

4.Glenn, T. 2016 NGS field guide: Overview. http://www.molecularecologist.com/next-gen-fieldguide-2016 (2016).

Quick, J. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016; 530: 228-232 [OpenAIRE] [PubMed] [DOI]

6.Hoenen, T. et al. Nanopore sequencing as a rapidly deployable ebola outbreak response tool. Emerg Infect Dis 22 (2015).

7.Faria, N. R. Zibra project: real-time sequencing of zika virus in brazil. https://nanoporetech.com/publications/zibra-project-real-time-sequencing-zika-virus-brazil (2016).

8.Parker, J., Helmstetter, A. J., Devey, D. S. & Papadopulos, A. S. T. Field-based species identification in eukaryotes using single molecule, real-time sequencing. bioRxiv (Cold Spring Harbor Labs Journals), doi:10.1101/107656 (2017).

Judge, K, Harris, SR, Reuter, S, Parkhill, J, Peacock, SJ. Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes. J. Antimicrob. Chemother.. 2015; 70: 2775-2778 [OpenAIRE] [PubMed] [DOI]

Greninger, AL. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Medicine. 2015; 7: 99 [OpenAIRE] [PubMed] [DOI]

11.Schmidt, K. et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. Journal of Antimicrobial Chemotherapy, doi:10.1093/jac/dkw397 (2016).

12.Istace, B. et al. de novo assembly and population genomic survey of natural yeast isolates with the oxford nanopore minion sequencer. bioRxiv (Cold Spring Harbor Labs Journals), doi:10.1101/066613 (2016).

Koren, S. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. 2012; 30: 693-700 [OpenAIRE] [PubMed] [DOI]

14.Koren, S., Walenz, B., Berlin, K., Miller, J. & AM, P. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, doi:10.1101/gr.215087.116 (2017).

15.Chin, C. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods, doi:10.1038/nmeth.4035 (2016).

27 references, page 1 of 2
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