Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

Bioinformatics

Volumn 32, Issue 17, 2016, Pages 2582-2589

  Sović, Ivan ^a   Križanović, Krešimir ^b   Skala, Karolj ^a   Šikić, Mile ^b,c  

^a RUDER BO KOVI INSTITUTE   (Croatia)

^b UNIVERSITY OF ZAGREB   (Croatia)

^c BIOINFORMATICS INSTITUTE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; DNA SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI K 12; HIGH THROUGHPUT SEQUENCING; NANOPORE;

ESCHERICHIA COLI; ESCHERICHIA COLI K12; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NANOPORES; SEQUENCE ANALYSIS, DNA;

EID: 84990876773     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw237     Document Type: Conference Paper

References (27)

1. Bankevich, A. et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol., 19, 455-477
2. Bankevich, A. and Pevzner, P.A. (2016) TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nat. Methods, 13, 248-250
3. Berlin, K. et al. (2015) Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol., 33, 623-630
4. Chaisson, M.J. and Tesler, G. (2012) Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application. BMC Bioinformatics, 13, 238
5. Chin, C.S. et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods, 10, 563-569
6. Gnerre, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. USA, 108, 1513-1518
7. Goldberg, S.M.D. et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. USA, 103, 11240-11245
8. Gurevich, A. et al. (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072-1075
9. Ip, C.L.C. et al. (2015) MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research, 4, 1075
10. Jain, M. et al. (2015) Improved data analysis for the MinION nanopore sequencer. Nat. Methods, 12, 351-356
11. Koren, S. et al. (2012) Hybrid error correction and de novo assembly of singlemolecule sequencing reads. Nat. Biotechnol., 30, 693-700
12. Kurtz, S. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12
13. Laver, T. et al. (2015) Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol. Detect. Quantif., 3, 1-8
14. Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]
15. Li, H. (2016) Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics, 32, 2103-2110
16. Liao, Y.C. et al. (2015) Completing bacterial genome assemblies: strategy and performance comparisons. Sci. Rep., 5, 8747
17. Loman, N.J. et al. (2015) A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods, 12, 733-735
18. Loman, N.J. and Quinlan, A.R. (2014) Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics, 30, 3399-3401
19. Miller, J.R. et al. (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics, 24, 2818
20. Myers, E.W. et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196-2204
21. Myers, E.W. (2005) The fragment assembly string graph. 21, 79-85
22. Myers, G. (2014) Efficient Local Alignment Discovery amongst Noisy Long Reads. In: Brown, D. and Morgenstern, B. (eds) Algorithms in Bioinformatics, Lecture Notes in Computer Science. Springer, Berlin, Heidelberg, pp. 52-67
23. Nagarajan, N. and Pop, M. (2013) Sequence assembly demystified. Nat. Rev. Genet., 14, 157-167
24. Pop, M. (2009) Genome assembly reborn: recent computational challenges. Brief. Bioinform., 10, 354-366
25. Quick, J. et al. (2014) A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer. Gigascience, 3, 22
26. Schirmer, M. et al. (2015) Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res., 43, e37
27. Sović, I. et al. (2016) Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap. Nat. Commun., 7, 11307