ANDES: Statistical tools for the analyses of deep sequencing

BMC Research Notes

Volumn 3, Issue , 2010, Pages

  Li, Kelvin ^a   Venter, Eli ^a   Yooseph, Shibu ^a   Stockwell, Timothy B ^a   Eckerle, Lance D ^b   Denison, Mark R ^b   Spiro, David J ^a   Methé, Barbara A ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955864524     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-3-199     Document Type: Article

References (16)

1. Genome sequencing in microfabricated high-density picolitre reactors. M Margulies M Egholm WE Altman S Attiya JS Bader LA Bemben J Berka MS Braverman YJ Chen Z Chen SB Dewell L Du JM Fierro XV Gomes BC Godwin W He S Helgesen CH Ho GP Irzyk SC Jando ML Alenquer TP Jarvie KB Jirage JB Kim JR Knight JR Lanza JH Leamon SM Lefkowitz M Lei J Li KL Lohman H Lu VB Makhijani KE McDade MP McKenna EW Myers E Nickerson JR Nobile R Plant BP Puc MT Ronan GT Roth GJ Sarkis JF Simons JW Simpson M Srinivasan KR Tartaro A Tomasz KA Vogt GA Volkmer SH Wang Y Wang MP Weiner P Yu RF Begley JM Rothberg, Nature 2005 437 7057 376 80 16056220
2. Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry. DR Bentley S Balasubramanian HP Swerdlow GP Smith J Milton CG Brown KP Hall DJ Evers, et al. Nature 2008 456 7218 53 59 10.1038/nature07517 18987734
3. The Bioperl toolkit: Perl modules for the life sciences. JE Stajich D Block K Boulez SE Brenner SA Chervitz C Dagdigian G Fuellen JG Gilbert I Korf H Lapp H Lehvslaiho C Matsalla CJ Mungall BI Osborne MR Pocock P Schattner M Senger LD Stein E Stupka MD Wilkinson E and Birney, Genome Res 2002 12 10 1611 8 10.1101/gr.361602 12368254
4. Biopython: freely available Python tools for computational molecular biology and bioinformatics. PJ Cock T Antao JT Chang BA Chapman CJ Cox A Dalke I Friedberg T Hamelryck F Kauff B Wilczynski MJ de Hoon, Bioinformatics 2009 25 11 1422 3 10.1093/bioinformatics/btp163 19304878
5. The Sequence Alignment/Map format and SAMtools. H Li B Handsaker A Wysoker T Fennell J Ruan N Homer G Marth G Abecasis R Durbin 1000 Genome Project Data Processing Subgroup, Bioinformatics 2009 25 16 2078 2079 10.1093/bioinformatics/btp352 19505943
6. ClustalW and ClustalX version 2. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez JD Thompson TJ Gibson DG Higgins, Bioinformatics 2007 23 21 2947 2948 10.1093/bioinformatics/btm404 17846036
7. RazerS-fast read mapping with sensitivity control. D Weese AK Emde T Rausch A Döring K Reinert, Genome Research 2009 19 1646 1654 10.1101/gr.088823.108 19592482
8. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. RC Edgar, BMC Bioinformatics 2004 5 113 15318951
9. Comparative genome assembly. M Pop A Phillippy AL Delcher SL Salzberg, Briefings in Bioinformatics 2004 5 3 237 248 10.1093/bib/5.3.237 15383210
10. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. A Cornish-Bowden, Nucleic Acids Res 1985 13 9 3021 3030 10.1093/nar/13.9.3021 2582368
11. Protein structure comparison. I Sillitoe CA Orengo, Bioinformatics: Genes, Proteins & Computers Towbridge, UK: Cromwell Press, Orengo CA, Jones DT, Thornton JM, 1 2003 81 101
12. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. R Development Core Team, 2005 http://www.R-project.org ISBN 3-900051-07-0
13. Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing. LD Eckerle MM Becker RA Halpin K Li E Venter X Lu S Scherbakova RL Graham RS Baric TB Stockwell DJ Spiro MR Denison, PLoS Pathogens 2010 6 5 10.1371/journal.ppat.1000896 20463816
14. High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. KA Eckert TA Kunkel, Nucleic Acids Research 1990 18 13 3739 3744 10.1093/nar/18.13.3739 2374708
15. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 403 410 2231712
16. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. V Kunin A Engelbrektson H Ochman P Hugenholtz, Environmental Microbiology 2009 19725865