The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Mavromatis, Konstantinos ^a   Land, Miriam L ^b   Brettin, Thomas S ^b   Quest, Daniel J ^b   Copeland, Alex ^a   Clum, Alicia ^a   Goodwin, Lynne ^c   Woyke, Tanja ^a   Lapidus, Alla ^a   Klenk, Hans Peter ^d   Cottingham, Robert W ^b   Kyrpides, Nikos C ^a  

^a DOE JOINT GENOME INSTITUTE   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; AUTOMATION; CONTIG MAPPING; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DNA BASE COMPOSITION; DNA SEQUENCE; DOWNSTREAM PROCESSING; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC ORGANIZATION; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; MICROBIAL GENETICS; MICROBIAL GENOME; NONHUMAN; PROTEIN ASSEMBLY; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

GENOME, BACTERIAL; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84871205244     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048837     Document Type: Article

References (19)

1. Sanger F, Nicklen S, Coulson AR, (1977) DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74: 5463-5467.
2. Elahi E, Ronaghi M, (2004) Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol Biol 255: 211-219 doi:10.1385/1-59259-752-1:211.
3. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, et al. (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6: 291-295 doi:10.1038/nmeth.1311.
4. Eid J, Fehr A, Gray J, Luong K, Lyle J, et al. (2009) Real-Time DNA Sequencing from Single Polymerase Molecules. Science 323: 133-138 doi:10.1126/science.1162986.
5. Chain PSG, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, et al. (2009) Genome Project Standards in a New Era of Sequencing. Science 326: 236-237 doi:10.1126/science.1180614.
6. Benjamini Y, Speed TP, (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40: e72 doi:10.1093/nar/gks001.
7. Aird D, Ross MG, Chen W-S, Danielsson M, Fennell T, et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12: R18 doi:10.1186/gb-2011-12-2-r18.
8. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119 doi:10.1186/1471-2105-11-119.
9. Besemer J, Borodovsky M, (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33: W451-4 doi:10.1093/nar/gki487.
10. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, et al. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7: 455-457 doi:10.1038/nmeth.1457.
11. Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: 1449-1452 doi:10.1126/science.1147112.
12. Pop M, (2009) Genome assembly reborn: recent computational challenges. Brief Bioinformatics 10: 354-366 doi:10.1093/bib/bbp026.
13. Nagarajan N, Pop M, (2009) Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol 16: 897-908 doi:10.1089/cmb.2009.0005.
14. Miller JR, Koren S, Sutton G, (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327 doi:10.1016/j.ygeno.2010.03.001.
15. Ribeiro F, Przybylski D, Yin S, Sharpe T, Gnerre S, et al. (2012) Finished bacterial genomes from shotgun sequence data. Genome research. Available:http://www.ncbi.nlm.nih.gov/pubmed/22829535. Accessed 2 September 2012.
16. Alkan C, Sajjadian S, Eichler EE, (2011) Limitations of next-generation genome sequence assembly. Nat Methods 8: 61-65 doi:10.1038/nmeth.1527.
17. Delcher AL, Salzberg SL, Phillippy AM, (2003) Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics Chapter 10: Unit 10.3 doi:10.1002/0471250953.bi1003s00.
18. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
19. Bao Z, Eddy SR, (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12: 1269-1276 doi:10.1101/gr.88502.