Toward a statistically explicit understanding of de novo sequence assembly

Bioinformatics

Volumn 29, Issue 23, 2013, Pages 2959-2963

  Howison, Mark ^a   Zapata, Felipe ^a   Dunn, Casey W ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; PROCEDURES; METHODOLOGY; REVIEW;

COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84890056084     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt525     Document Type: Review

References (36)

1. Alkan, C. et al. (2011) Limitations of next-generation genome sequence assembly. Nat. Methods, 8, 61-65.
2. Bansal, V. et al. (2008) An MCMC algorithm for haplotype assembly from wholegenome sequence data. Genome Res., 18, 1336-1346.
3. Bradnam, K.R. et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2, 10.
4. Browning, S.R. and Browning, B.L. (2011) Haplotype phasing: existing methods and new developments. Nat. Rev. Genet., 12, 703-714.
5. Chain, P.S. et al. (2009) Genomics. Genome project standards in a new era of sequencing. Science, 326, 236-237.
6. Charuvaka, A. and Rangwala, H. (2011) Evaluation of short read metagenomic assembly. BMC Genomics, 12, S8.
7. Clark, S.C. et al. (2013) ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics, 29, 435-443.
8. Earl, D. et al. (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res., 21, 2224-2241.
9. Finotello, F. et al. (2012) Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. Brief. Bioinform., 13, 269-280.
10. Giardine, B. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
11. Gilks, W.R. et al. (1995) Markov Chain Monte Carlo in Practice. Chapman and Hall/CRC, London.
12. 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.
13. Holder, M.T. et al. (2008) A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Syst. Biol., 57, 814-821.
14. Howison, M. et al. (2012) BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance. In: Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP'12). Boston, MA, USA.
15. Hunt, M. et al. (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biol., 14, R47.
16. Iqbal, Z. et al. (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet., 44, 226-232.
17. Jaffe, D.B. et al. (2012) The FASTG Format Specification (v1.00). http://fastg.sourceforge.net/FASTG-Spec-v1.00.pdf. (27 February 2013, date last accessed).
18. Li, Y. et al. (2010) State of the art de novo assembly of human genomes from massively parallel sequencing data. Hum. Genomics, 4, 271-277.
19. Li, H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28, 1838-1844.
20. Mardis, E. et al. (2002) What is finished, and why does it matter. Genome Res., 12, 669-671.
21. Medvedev, P. and Brudno, M. (2009) Maximum likelihood genome assembly. J. Comput. Biol., 16, 1101-1116.
22. Miller, J.R. et al. (2010) Assembly algorithms for next-generation sequencing data. Genomics, 95, 315-327.
23. Nagarajan, N. and Pop, M. (2013) Sequence assembly demystified. Nat. Rev. Genet., 14, 157-167.
24. Nielsen, R. et al. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451.
25. Paszkiewicz, K. and Studholme, D.J. (2010) De novo assembly of short sequence reads. Brief. Bioinform., 11, 457-472.
26. Phillippy, A. et al. (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol., 9, R55.
27. Rahman, A. and Pachter, L. (2013) CGAL: computing genome assembly likelihoods. Genome Biol., 14, R8.
28. Ricker, N. et al. (2012) The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics, 100, 167-175.
29. Salzberg, S.L. and Yorke, J.A. (2005) Beware of mis-assembled genomes. Bioinformatics, 21, 4320-4321.
30. Salzberg, S.L. et al. (2012) GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res., 22, 557-567.
31. Schatz, M.C. et al. (2010) Assembly of large genomes using second-generation sequencing. Genome Res., 20, 1165-1173.
32. Simpson, J.T. and Durbin, R. (2012) Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-556.
33. Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
34. Varma, A. et al. (2011) An improved maximum likelihood formulation for accurate genome assembly. In: Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). Orlando, FL, USA, pp. 165-170.
35. Wu, Y.-W. et al. (2012) Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Bioinformatics, 28, i363-i369.
36. Zimin, A.V. et al. (2008) Assembly reconciliation. Bioinformatics, 24, 42-45.