Comparison of genome sequencing technology and assembly methods for the analysis of a GC-rich bacterial genome

Current Microbiology

Volumn 70, Issue 3, 2014, Pages 338-344

  Scott, Derrick ^a   Ely, Bert ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; RESTRICTION ENDONUCLEASE;

ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; BACTERIAL GENOME; CAULOBACTER; CAULOBACTER HENRICII; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; DNA BASE COMPOSITION; GC RICH SEQUENCE; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC ANALYSIS; GENOME SEQUENCING TECHNOLOGY; IMMUNOASSAY ANALYZER; NONHUMAN; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE ANALYSIS; ALPHAPROTEOBACTERIA; BIOLOGY; DNA SEQUENCE; GENETICS; PROCEDURES;

BACTERIA (MICROORGANISMS); CAULOBACTER HENRICII;

ALPHAPROTEOBACTERIA; BASE COMPOSITION; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; SEQUENCE ANALYSIS, DNA;

EID: 84949133558     PISSN: 03438651     EISSN: 14320991     Source Type: Journal    
DOI: 10.1007/s00284-014-0721-6     Document Type: Article

References (24)

1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
2. Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD (2011) Generation of Multimillion-Sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol. 77: 3846-3852.
3. bio. biomedicine. gu. se/cutter2/. Accessed 2014.
4. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10: 563-569.
5. Consortium, T. H. M. P (2012) A framework for human microbiome research. Nature 486: 215-221.
6. Consortium, T. H. M. P (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
7. Darling AE, Mau B, Perna NT (2010) ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147.
8. Ely B, Gerardot CJ (1988) Use of pulsed-field-gradient gel electrophoresis to construct a physical map of the Caulobacter crescentus genome. Gene 68: 323-333.
9. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
10. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075.
11. Jackman SD, Birol I (2010) Assembling genomes using shortread sequencing technology. Genome Biol 11: 202.
12. Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, McVey SD, Radune D, Bergman NH, Phillippy AM (2013) Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 14: R101.
13. Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL (2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics 29: 1718-1725.
14. 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.
15. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA et al (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
16. Narzisi G, Mishra B (2011) Comparing de novo genome assembly: the long and short of it. PLoS ONE 6: e19175.
17. Phillippy AM, Schatz MC, Pop M (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 9: R55.
18. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genom 13: 341.
19. Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M (2011) Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform 14: 213-224.
20. Shin SC, Ahn do H, Kim SJ, Lee H, oh TJ, Lee JE, Park H (2013) Advantages of single-molecule real-time sequencing in high-GC content genomes. PLoS One 8: e68824.
21. www. illumina. com. Accessed 2014.
22. www. pacificbiosciences. com. Accessed 2014.
23. www. qiagen. com. Accessed 2014.
24. Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013) The MaSuRCA genome assembler. Bioinformatics 29: 2669-2677.