Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Desai, Aarti ^a   Marwah, Veer Singh ^a   Yadav, Akshay ^a   Jha, Vineet ^a   Dhaygude, Kishor ^a   Bangar, Ujwala ^a   Kulkarni, Vivek ^a   Jere, Abhay ^a  

^a PERSISTENT SYSTEMS LTD   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; CAENORHABDITIS ELEGANS; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENOME SIZE; HIGH THROUGHPUT SEQUENCING; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROCESS TECHNOLOGY; SACCHAROMYCES; SACCHAROMYCES KUDRIAVZEVII; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDITY;

ANIMALS; CAENORHABDITIS ELEGANS; DATABASES, NUCLEIC ACID; ESCHERICHIA COLI; GENOME; SACCHAROMYCES; SEQUENCE ANALYSIS, DNA;

EID: 84876082278     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060204     Document Type: Article

References (43)

1. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, et al. (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326 (5954): 865-867.
2. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298 (5591): 129-149.
3. Lander ES, Linton LM, Birren B, Nusbaum C, The International Human Genome Consortium, et al. (2001) Initial sequencing and analysis of the human genome. Nature, Vol. 409 (6822): 860-921.
4. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol. 26: 1135-1145.
5. Metzker ML, (2010) Sequencing technologies - the next generation. Nat Rev Genet. 11: 31-46.
6. Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol. 10 (9): R94.
7. Garg R, Patel RK, Tyagi AK, Jain M, (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 18 (1): 53-63.
8. Tantia MS, Vijh RK, Sikka P Vij PK Kataria RS, et al. (2011) Whole-genome sequence assembly of the water buffalo (Bubalus bubalis). Indian Journal of Animal Sciences 81 (5): 38-47.
9. Huse SM, Ye Y, Zhou Y, Fodor AA, (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One 7 (6): e34242.
10. Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486 (7402): 207-214.
11. Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467 (7319): 1061-1073.
12. Rödelsperger C, Krawitz P, Bauer S, Hecht J, Bigham AW, et al. (2011) Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders. Bioinformatics 27 (6): 829-836.
13. Chaki M, Airik R, Ghosh AK, Giles RH, Chen R, et al. (2012) Exome Capture Reveals ZNF423 and CEP164 Mutations, Linking Renal Ciliopathies to DNA Damage Response Signaling. 150 (3): 533-548.
14. Wang JL, Yang X, Xia K, Hu ZM, Weng L, et al. (2010) TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain 133 (Pt 12): 3510-3518.
15. Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, (2011) Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics 27: i383-i391.
16. Costa V, Angelini C, De Feis I, Ciccodicola A, (2010) Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol. 2010: 853916.
17. Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, et al. (2012) Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis. PLoS One 7 (7): e41528.
18. Wang J, Cao X, Zhang Y, Su B, (2012) Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates. BMC Evol Biol. 12: 144.
19. Yu W, Jin C, Lou X, Han X, Li L, et al. (2011) Global analysis of DNA methylation by Methyl-Capture sequencing reveals epigenetic control of cisplatin resistance in ovarian cancer cell. PLoS One 6 (12): e29450.
20. Kircher M, Stenzel U, Kelso J, (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol. 10 (8): R83.
21. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475 (7356): 348-352.
22. Haiminen N, Kuhn DN, Parida L, Rigoutsos I, (2011) Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PLoS One 6 (9): e24182.
23. Lin Y, Li J, Shen H, Zhang L, Papasian CJ, et al. (2011) Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 27 (15): 2031-2037.
24. Zhang W, Chen J, Yang Y, Tang Y, Shang J, et al. (2011) A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One 6 (3): e17915.
25. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10 (3): R32.
26. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (7057): 376-380.
27. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20 (2): 265-272.
28. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18 (5): 821-829.
29. Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, et al. (2011) Meraculous: de novo genome assembly with short paired-end reads. PLoS One 6 (8): e23501.
30. 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, Vol. 28 (11): 1420-1428.
31. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res. 19 (6): 1117-1123.
32. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108 (4): 1513-1518.
33. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287 (5461): 2196-2204.
34. Boisvert S, Laviolette F, Corbeil J, (2010) Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol. 17 (11): 1519-1533.
35. Warren RL, Sutton GG, Jones SJ, Holt RA, (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics, Vol. 23 (4): 500-501.
36. Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, et al. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23 (21): 2942-2944.
37. Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, et al. (2011) The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1 (1): 11-25.
38. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, et al. (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5 (2): 183-188.
39. Schatz MC, Delcher AL, Salzberg SL, (2010) Assembly of large genomes using second-generation sequencing. Genome Res. 20 (9): 1165-1173.
40. Pevzner PA, Tang H, Waterman MS, (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A, Vol. 98 (17): 9748-9753.
41. Miller JR, Koren S, Sutton G, (2010) Assembly algorithms for next-generation sequencing data. Genomics 95 (6): 315-327.
42. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22 (3): 557-567.
43. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5 (2): R12 doi:10.1186/gb-2004-5-2-r12.