An extended genovo metagenomic assembler by incorporating paired-end information

PeerJ

Volumn 2013, Issue 1, 2013, Pages

  Afiahayati, ^a   Sato, Kengo ^a   Sakakibara, Yasubumi ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

454 paired end reads; de novo metagenomic assembler; Genovo

Indexed keywords

ARTICLE; BIOINFORMATICS; BIOLOGY; COMPUTER MODEL; CONSENSUS SEQUENCE; CONTIG MAPPING; GENETIC DISTANCE; GENETIC IDENTIFICATION; METAGENOME; NONHUMAN; PROBABILITY; SAMPLING; SIMULATION; STATISTICAL DISTRIBUTION; VIRUS ASSEMBLY;

EID: 84888378526     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.196     Document Type: Article

References (28)

1. Aldous DJ. 1985. Exchangeability and related topics. In: Hennequin PL, ed. cole d't de probabilits de Saint Flour XIII 1983, Lecture Notes in Mathematics. Berlin: Springer. 1117:1198.
2. Chen K, Pachter L. 2005. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology 1(2):e24.
3. Degroot MH, Schervish MJ. 2011. Probability and statistics. Boston: Addison-Wesley Publishing.
4. Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. 2010. Parallel, tag-directed assembly of locally derived short sequence reads. Nature Methods 7(2):199-122.
5. Johnson M. Chinese Restaurants Process. Available at http://cog.brown.edu/~mj/classes/cg168/slides/ChineseRestaurants.pdf (accessed 10 May 2012).
6. Koren S, Treangen TJ, Pop M. 2011. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21):2964-2971.
7. Lai B, Ding R, Li Y, Duan L, Zhu H. 2012. A de novo metagenomic assembly program for shotgun dna reads. Bioinformatics 28(11):1455-1462.
8. Laserson J, Jojic V, Koller D. 2011. Genovo: de novo assembly for metagenomes. Journal of Computational Biology 18(3):429-443.
9. Lasken RS, Stockwell TB. 2007. Mecanishm of chimera formation during the multiple displacement amplification reaction. BMC Biotechnology 7:19.
10. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research 20:265-272.
11. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
12. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M et al. 2007. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4(6):495-500.
13. Mende DR, Waller AS, Sunagawa S, Jrvelin AI, Chan MM, Arumugam M, Raes J, Bork P. 2012. Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE 7(2):e31386.
14. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. 2009. Sequencing and de novo analysis of a coral larval transcriptome using 454 gsflx. BMC Genomics 10:219.
15. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24(24):2818-2824.
16. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KHJ, Remington KA et al. 2000. A Whole-Genome Assembly of Drosophila. Science 287(5461):2196-2204.
17. Nagarajan N, Pop M. 2013. Sequence assembly demystified. Nature Reviews Genetics 14:157-167.
18. 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 Research 40(20):e155.
19. Peng Y, Leung HCM, Yiu SM, Chin FYL. 2010. IDBA a practical iterative de bruijn graph de novo assembler. In: Berger B, ed. Research in computational molecular biology, Lecture Notes in Computer Science. Berlin: Springer. 426-440.
20. Peng Y, Leung HCM, Yiu SM, Chin FYL. 2011. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 27(13):i94-101.
21. Peng Y, Leung HC, Yiu SM, Chin FY. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11):1420-1428.
22. Pigmatelli M, Moya A. 2011. Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS ONE 6(5):e19984.
23. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59-65.
24. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. 2008. Metasim a sequencing simulator for genomics and metagenomics. PLoS ONE 3(10):e3373.
25. Scholz MB, Lo CC, Chain PS. 2012. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current Opinion in Biotechnology 23(1):9-15.
26. Unterseher M, Jumpponen A, Opik M, Tedersoo L, Moora M, Dormann CF, Schnittler M. 2011. Species abundance distributions and richness estimations in fungal metagenomics lessons learned from community ecology. Molecular Ecology 20:275-285.
27. Zerbino D, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de bruijn graphs. Genome Research 18:821-829.
28. Zerbino DR, McEwen GK, Margulies EH, Birney E. 2009. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS ONE 4:e8407.