PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

Abstract

Low-cost DNA sequencing technologies have expanded the role for direct nucleic acid sequencing in the analysis of genomes, transcriptomes, and the metagenomes of whole ecosystems. Human and machine comprehension of such large datasets can be simplified via synthesis of sequence fragments into long, contiguous blocks of sequence (contigs), but most of the progress in the field of assembly has focused on genomes in isolation rather than metagenomes. Here, we present software for paired-read iterative contig extension (PRICE), a strategy for focused assembly of particular nucleic acid species using complex metagenomic data as input. We describe the assembly strategy implemented by PRICE and provide examples of its application to the sequence of particular genes, transcripts, and virus genomes from complex multicomponent datasets, including an assembly of the BCBL-1 strain of Kaposi’s sarcoma-associated herpesvirus. PRICE is open-source and available for free download (derisilab.ucsf.edu/software/price/ or sourceforge.net/projects/pricedenovo/).

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References 64

1. 1.
   Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries · 2011

   No notice
2. 2.

   Altschul S. F. Gish W. Miller W. Myers E. W. Lipman D. J., 1990 Basic local alignment search tool. J. Mol. Biol. 215: 403–410

   Not in our library10.1016/s0022-2836(05)80360-2

3. 3.

   Ariyaratne P. N. Sung W.-K., 2011 PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics 27: 167–174

   Not in our library10.1093/bioinformatics/btq626

4. 4.

   Arron S. T. Ruby J. G. Dybbro E. Ganem D. Derisi J. L., 2011 Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma. J. Invest. Dermatol. 131: 1745–1753

   Not in our library10.1038/jid.2011.91

5. 5.

   Bechtel J. T. Liang Y. Hvidding J. Ganem D., 2003 Host range of Kaposi’s sarcoma-associated herpesvirus in cultured cells. J. Virol. 77: 6474–6481

   Not in our library10.1128/jvi.77.11.6474-6481.2003

6. 6.

   Bexfield N. Kellam P., 2011 Metagenomics and the molecular identification of novel viruses. Vet. J. 190: 191–198

   Not in our library10.1016/j.tvjl.2010.10.014

7. 7.

   Butler J. MacCallum I. Kleber M. Shlyakhter I. A. Belmonte M. K., 2008 ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18: 810–820

   Not in our library10.1101/gr.7337908

8. 8.

   Chaisson M. J. Brinza D. Pevzner P. A., 2009 De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res. 19: 336–346

   Not in our library10.1101/gr.079053.108

9. 9.

   Chandriani S. Skewes-Cox P. Zhong W. Ganem D. E. Divers T. J., 2013 Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis. Proc. Natl. Acad. Sci. U S A. (in press) 10.1073/pnas.1219217110.

   Not in our library10.1073/pnas.1219217110

10. 10.

    Dobrindt U. Hochhut B. Hentschel U. Hacker J., 2004 Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2: 414–424

    Not in our library10.1038/nrmicro884

11. 11.

    Earl D. Bradnam K. St John J. Darling A. Lin D., 2011 Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 21: 2224–2241

    Not in our library10.1101/gr.126599.111

12. 12.
    Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads · 2011

    No notice
13. 13.

    Ferragina P. Manzini G., 2001 An experimental study of an opportunistic index, pp. 269–278 in SODA ’01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms. Society for Industrial and Applied Mathematics, Philadelphia

    Not in our library

14. 14.

    Glenn T. C., 2011 Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11: 759–769

    Not in our library10.1111/j.1755-0998.2011.03024.x

15. 15.

    Grabherr M. G. Haas B. J. Yassour M. Levin J. Z. Thompson D. A., 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29: 644–652

    Not in our library10.1038/nbt.1883

16. 16.
    A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa · 2012

    Corrected
17. 17.

    Grossmann C. Ganem D., 2008 Effects of NFkappaB activation on KSHV latency and lytic reactivation are complex and context-dependent. Virology 375: 94–102

    Not in our library10.1016/j.virol.2007.12.044

18. 18.

    Hansen K. D. Brenner S. E. Dudoit S., 2010 Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 38: e131

    Not in our library10.1093/nar/gkq224

19. 19.

    Hernandez D. François P. Farinelli L. Osterås M. Schrenzel J., 2008 De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18: 802–809

    Not in our library10.1101/gr.072033.107

20. 20.

    Hiatt J. B. Patwardhan R. P. Turner E. H. Lee C. Shendure J., 2010 Parallel, tag-directed assembly of locally derived short sequence reads. Nat. Methods 7: 119–122

    Not in our library10.1038/nmeth.1416

21. 21.

    Holmes T. C. May A. E. Zaleta-Rivera K. Ruby J.G. Skewes-Cox P., 2012 Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor. J. Am. Chem. Soc. 134: 17797–17806

    Not in our library10.1021/ja308622d

22. 22.

    Hossain M. S. Azimi N. Skiena S., 2009 Crystallizing short-read assemblies around seeds. BMC Bioinformatics 10(Suppl 1): S16

    Not in our library10.1186/1471-2105-10-s1-s16

23. 23.

    Jones D. M. McLauchlan J., 2010 Hepatitis C virus: assembly and release of virus particles. J. Biol. Chem. 285: 22733–22739

    Not in our library10.1074/jbc.r110.133017

24. 24.

    Kärkkäinen J. Sanders P., 2003 Simple Linear Work Suffix Array Construction, pp. 943–955 in Automata, Languages and Programming, edited by Baeten J. C. M. Lenstra J. K. Parrow J. Woeginger G. J. Springer Berlin Heidelberg, Berlin, Heidelberg

    Not in our library

25. 25.

    Kaysser L. Bernhardt P. Nam S.-J. Loesgen S. Ruby J. G., 2012 Merochlorins a-d, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases. J. Am. Chem. Soc. 134: 11988–11991

    Not in our library10.1021/ja305665f

26. 26.
    Quake: quality-aware detection and correction of sequencing errors · 2010

    No notice
27. 27.

    Kent W. J., 2002 BLAT–the BLAST-like alignment tool. Genome Res. 12: 656–664

    Not in our library10.1101/gr.229202

28. 28.

    Lagunoff M. Bechtel J. Venetsanakos E. Roy A.-M. Abbey N., 2002 De novo infection and serial transmission of Kaposi’s sarcoma-associated herpesvirus in cultured endothelial cells. J. Virol. 76: 2440–2448

    Not in our library10.1128/jvi.76.5.2440-2448.2002

29. 29.

    Lander E., 2005 Biology as Information, pp. 373–373 in Research in Computational Molecular Biology, edited by Miyano S. Mesirov J. Kasif S. Istrail S. Pevzner P. A. Springer Berlin Heidelberg, Berlin, Heidelberg

    Not in our library

30. 30.

    Lander E. S. Waterman M. S., 1988 Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2: 231–239

    Not in our library10.1016/0888-7543(88)90007-9

31. 31.
    Quasispecies Theory and the Behavior of RNA Viruses · 2010

    No notice
32. 32.

    Lawrence J. G. Roth J. R., 1996 Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843–1860

    Not in our library10.1093/genetics/143.4.1843

33. 33.

    Li H. Homer N., 2010 A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 11: 473–483

    Not in our library10.1093/bib/bbq015

34. 34.

    Li R. Fan W. Tian G. Zhu H. He L., 2010 a The sequence and de novo assembly of the giant panda genome. Nature 463: 311–317

    Not in our library10.1038/nature08696

35. 35.

    Li R. Zhu H. Ruan J. Qian W. Fang X., 2010 b De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20: 265–272

    Not in our library10.1101/gr.097261.109

36. 36.

    Mahony J. B. Petrich A. Smieja M., 2011 Molecular diagnosis of respiratory virus infections. Crit. Rev. Clin. Lab. Sci. 48: 217–249

    Not in our library10.3109/10408363.2011.640976

37. 37.
    Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution · 2013

    No notice
38. 38.

    Namiki T. Hachiya T. Tanaka H. Sakakibara Y., 2012 MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40: e155

    Not in our library10.1093/nar/gks678

39. 39.

    Needleman S. B. Wunsch C. D., 1970 A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48: 443–453

    Not in our library10.1016/0022-2836(70)90057-4

40. 40.

    Peng Y. Leung H. C. M. Yiu S. M. Chin F. Y. L., 2011 Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 27: i94–i101

    Not in our library10.1093/bioinformatics/btr216

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