Scaffolding and completing genome assemblies in real-time with nanopore sequencing

Nature Communications

Volumn 8, Issue , 2017, Pages

  Cao, Minh Duc ^a   Nguyen, Son Hoang ^a   Ganesamoorthy, Devika ^a   Elliott, Alysha G ^a   Cooper, Matthew A ^a   Coin, Lachlan J M ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; ERROR ANALYSIS; EUKARYOTE; GENOME; MOLECULAR ANALYSIS; REAL TIME;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; GENE SEQUENCE; GENETIC ANALYSIS; KLEBSIELLA PNEUMONIAE; NANOPORE; NONHUMAN; SACCHAROMYCES CEREVISIAE; SALMONELLA ENTERICA SEROVAR TYPHI; ALGORITHM; BIOLOGY; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; PROCEDURES; REPRODUCIBILITY; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); EUKARYOTA;

BACTERIAL DNA;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; GENOME, BACTERIAL; KLEBSIELLA PNEUMONIAE; NANOPORES; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 85013288071     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms14515     Document Type: Article

References (42)

1. Ashton, P. M. et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol. 33, 296-300 (2015).
2. Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770-13773 (1996).
3. Branton, D. et al. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146-1153 (2008).
4. Stoddart, D., Heron, A. J., Mikhailova, E., Maglia, G. & Bayley, H. Singlenucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc. Natl Acad. Sci. USA 106, 7702-7707 (2009).
5. Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-Read SMRT sequencing data. Nat. Methods 10, 563-569 (2013).
6. Loman, N. J., Quick, J. & Simpson, J. T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12, 733-735 (2015).
7. Berlin, K. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623-630 (2015).
8. Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103-2110 (2016).
9. Koren, S. et al. Hybrid error correction and de novo assembly of singlemolecule sequencing reads. Nat. Biotechnol. 30, 693-700 (2012).
10. Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res. 25, 1750-1756 (2015).
11. Madoui, M.-A. et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 16, 327 (2015).
12. Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012).
13. Boetzer, M. & Pirovano, W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics 15, 211 (2014).
14. Karlsson, E., Lärkeryd, A., Sjödin, A., Forsman, M. & Stenberg, P. Scaffolding of a bacterial genome using MinION nanopore sequencing. Sci. Rep. 5, 11996 (2015).
15. Warren, R. L. et al. LINKS: scalable, alignment-free scaffolding of draft genomes with long reads. GigaScience 4, 35 (2015).
16. Castro-Wallace, S. L. et al. Nanopore DNA Sequencing and Genome Assembly on the International Space Station. Preprint at bioRxiv. doi: https://doi.org/10.1101/077651 (2016).
17. Istace, B. et al. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. Preprint at bioRxiv. doi: https://doi.org/10.1101/066613 (2016).
18. Treangen, T. J. & Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet. 13, 36-46 (2012).
19. Cao, M. D. et al. Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing. GigaScience 5, 32 (2016).
20. Loman, N. J. & Quinlan, A. R. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 30, 3399-3401 (2014).
21. Jain, M. et al. Improved data analysis for the MinION nanopore sequencer. Nat. Methods 12, 351-356 (2015).
22. Cao, M. D., Ganesamoorthy, D., Cooper, M. A. & Coin, L. J. M. Realtime analysis and visualization of MinION sequencing data with npReader. Bioinformatics 32, 764-766 (2016).
23. Carattoli, A. et al. In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob. Agents. Chemother. 58, 3895-3903 (2014).
24. Hudson, C. M., Bent, Z. W., Meagher, R. J. & Williams, K. P. Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLoS ONE 9, e99209 (2014).
25. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014).
26. Langille, M. G. I., Hsiao, W. W. L. & Brinkman, F. S. L. Detecting genomic islands using bioinformatics approaches. Nat. Rev. Microbiol. 8, 373-382 (2010).
27. Mantri, Y. & Williams, K. P. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res. 32, D55-D58 (2004).
28. Zhou, Y., Liang, Y., Lynch, K. H., Dennis, J. J. & Wishart, D. S. PHAST: a fast phage search tool. Nucleic Acids Res. 39, W347-W352 (2011).
29. Quick, J., Quinlan, A. R. & Loman, N. J. A reference bacterial genome dataset generated on the {MinION} portable single-molecule nanopore sequencer. GigaScience 3, 22 (2014).
30. Myers, E. W. et al. A whole-genome assembly of drosophila. Science 287, 2196-2204 (2000).
31. Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
32. Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072-1075 (2013).
33. Bashir, A. et al. A hybrid approach for the automated finishing of bacterial genomes. Nat. Biotechnol. 30, 701-707 (2012).
34. Deshpande, V., Fung, E. D. K., Pham, S. & Bafna, V. Algorithms in Bioinformatics, Vol. 8126, 349-363 (Springer Berlin Heidelberg, 2013).
35. David, M., Dursi, L. J., Yao, D., Boutros, P. C. & Simpson, J. T. Nanocall: an open source basecaller for Oxford Nanopore sequencing data. Bioinformatics 33, 49-55 (2016).
36. Boža, V., Broňa, B. & Vinǎr, T. DeepNano: Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads. Preprint at arXiv: 1603.09195 (2016).
37. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
38. Koren, S. & Phillippy, A. M. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23, 110-120 (2015).
39. Kruskal, J. B. On the shortest spanning subtree of a graph and the traveling salesman problem. Proc. Am. Math. Soc. 7, 48 (1956).
40. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv: 1303.3997 (2013).
41. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
42. Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640-2644 (2012).