Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes

Genomics

Volumn 100, Issue 5, 2012, Pages 271-276

  Tae, Hongseok ^a   Settlage, Robert E ^a   Shallom, Shamira ^a   Bavarva, Jasmin H ^a   Preston, Dale ^b   Hawkins, Gregory N ^b   Adams, L Garry ^c   Garner, Harold R ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b Texas Animal Health Commission   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Brucella; Comparative genomics; Iterative mapping; Resequencing; Sequence assembly; Variant calling

Indexed keywords

ANIMAL TISSUE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; BRUCELLA SUIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE MAPPING; GENE SEQUENCE; GENETIC ORGANIZATION; GENETIC VARIABILITY; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REPEAT PROCEDURE; STRAIN DIFFERENCE;

BASE SEQUENCE; BRUCELLA SUIS; CLUSTER ANALYSIS; GENETIC TECHNIQUES; GENETIC VARIATION; GENOME, BACTERIAL; INDEL MUTATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

BACTERIA (MICROORGANISMS); BRUCELLA; BRUCELLA MELITENSIS BIOVAR SUIS; BRUCELLA SUIS 1330;

EID: 84867919242     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2012.07.015     Document Type: Article

References (20)

1. Drake J.W., Charlesworth B., Charlesworth D., Crow J.F. Rates of spontaneous mutation. Genetics 1998, 148:1667-1686.
2. Simpson J.T., Wong K., Jackman S.D., Schein J.E., Jones S.J., Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009, 19:1117-1123.
3. Tsai I.J., Otto T.D., Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 2010, 11:R41.
4. Otto T.D., Sanders M., Berriman M., Newbold C. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010, 26:1704-1707.
5. Glynn M.K., Lynn T.V. Brucellosis. J. Am. Vet. Med. Assoc. 2008, 223:900-908.
6. Young E.J. An overview of human brucellosis. Clin. Infect. Dis. 1995, 21:283-289.
7. DelVecchio V.G., Kapatral V., Redkar R.J., Patra G., Mujer C., Los T., Ivanova N., Anderson I., Bhattacharyya A., Lykidis A., Reznik G., Jablonski L., Larsen N., D'Souza M., Bernal A., Mazur M., Goltsman E., Selkov E., Elzer P.H., Hagius S., O'Callaghan D., Letesson J.-J., Haselkorn R., Kyrpides N., Overbeek R. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:443-448.
8. Alton G.G., Jones L.M., Angus R.D., Verger J.M. Techniques for the Brucellosis Laboratory 1988, INRA, Paris.
9. Paulsen I.T., Seshadri R., Nelson K.E., Eisen J.A., Heidelberg J.F., Read T.D., Dodson R.J., Umayam L., Brinkac L.M., Beanan M.J., Daugherty S.C., Deboy R.T., Durkin A.S., Kolonay J.F., Madupu R., Nelson W.C., Ayodeji B., Kraul M., Shetty J., Malek J., Aken S.E.V., Riedmuller S., Tettelin H., Gill S.R., White O., Salzberg S.L., Hoover D.L., Lindler L.E., Halling S.M., Boyle S.M., Fraser C.M. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:13148-13153.
10. Lavigne J.-P., Vergunst A.C., Bourg G., O'Callaghan D. The IncP island in the genome of Brucella suis 1330 was acquired by site-specific integration. Infect. Immun. 2005, 73:7779-7783.
11. Wattam A.R., Williams K.P., Snyder E.E., Almeida N.F., Shukla M., Dickerman A.W., Crasta O.R., Kenyon R., Lu J., Shallom J.M., Yoo H., Ficht T.A., Tsolis R.M., Munk C., Tapia R., Han C.S., Detter J.C., Bruce D., Brettin T.S., Sobral B.W., Boyle S.M., Setubal J.C. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J. Bacteriol. 2009, 191:3569-3579.
12. Tae H., Shallom S., Settlage R., Preston D., Adams L.G., Garner H.R. Revised genome sequence of Brucella suis 1330. J. Bacteriol. 2011, 193:6410.
13. Halling S.M., Tatum F.M., Bricker B.J. Sequence and characterization of an insertion sequence, IS711, from Brucella ovis. Gene 1993, 133:123-127.
14. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
15. Lunter G., Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011, 21:936-939.
16. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
17. Wei Z., Wang W., Hu P., Lyon G.J., Hakonarson H. SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res. 2011, 39:e132.
18. Li H., Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595.
19. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20:1297-1303.
20. Ye K., Schulz M.H., Long Q., Apweiler R., Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25:2865-2871.