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Items: 1 to 20 of 93


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

Tae H, Settlage RE, Shallom S, Bavarva JH, Preston D, Hawkins GN, Adams LG, Garner HR.

Genomics. 2012 Nov;100(5):271-6. doi: 10.1016/j.ygeno.2012.07.015. Epub 2012 Aug 10.


The challenge of detecting indels in bacterial genomes from short-read sequencing data.

Steglich M, Nübel U.

J Biotechnol. 2017 May 20;250:11-15. doi: 10.1016/j.jbiotec.2017.02.026. Epub 2017 Mar 4.


Performance evaluation of indel calling tools using real short-read data.

Hasan MS, Wu X, Zhang L.

Hum Genomics. 2015 Aug 19;9:20. doi: 10.1186/s40246-015-0042-2.


Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.


Complete genome sequence of Brucella suis field strain BCB025 of sequence type ST22.

Ke Y, Wang Y, Yuan X, Xu J, Zhen Q, Wang Z, Li T, Wang D, Huang L, Song H, Chen Z.

J Bacteriol. 2012 Dec;194(24):6959. doi: 10.1128/JB.01814-12.


Revised genome sequence of Brucella suis 1330.

Tae H, Shallom S, Settlage R, Preston D, Adams LG, Garner HR.

J Bacteriol. 2011 Nov;193(22):6410. doi: 10.1128/JB.06181-11.


Genetic variation in the Staphylococcus aureus 8325 strain lineage revealed by whole-genome sequencing.

Bæk KT, Frees D, Renzoni A, Barras C, Rodriguez N, Manzano C, Kelley WL.

PLoS One. 2013 Sep 30;8(9):e77122. doi: 10.1371/journal.pone.0077122. eCollection 2013.


Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis.

Halling SM, Peterson-Burch BD, Bricker BJ, Zuerner RL, Qing Z, Li LL, Kapur V, Alt DP, Olsen SC.

J Bacteriol. 2005 Apr;187(8):2715-26.


Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes.

Yeo ZX, Wong JC, Rozen SG, Lee AS.

BMC Genomics. 2014 Jun 24;15:516. doi: 10.1186/1471-2164-15-516.


Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

Otto TD, Sanders M, Berriman M, Newbold C.

Bioinformatics. 2010 Jul 15;26(14):1704-7. doi: 10.1093/bioinformatics/btq269. Epub 2010 Jun 18.


A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.


Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer.

Yeo ZX, Chan M, Yap YS, Ang P, Rozen S, Lee AS.

PLoS One. 2012;7(9):e45798. doi: 10.1371/journal.pone.0045798. Epub 2012 Sep 19.


Complete genome sequence of Brucella suis VBI22, isolated from bovine milk.

Tae H, Shallom S, Settlage R, Hawkins GN, Adams LG, Garner HR.

J Bacteriol. 2012 Feb;194(4):910. doi: 10.1128/JB.06556-11.


SOAPindel: efficient identification of indels from short paired reads.

Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J.

Genome Res. 2013 Jan;23(1):195-200. doi: 10.1101/gr.132480.111. Epub 2012 Sep 12.


Whole-genome mapping reveals a large chromosomal inversion on Iberian Brucella suis biovar 2 strains.

Ferreira AC, Dias R, de Sá MIC, Tenreiro R.

Vet Microbiol. 2016 Aug 30;192:220-225. doi: 10.1016/j.vetmic.2016.07.024. Epub 2016 Aug 1.


Development of a multiplex PCR assay for polymorphism analysis of Brucella suis biovars causing brucellosis in swine.

Ferrão-Beck L, Cardoso R, Muñoz PM, de Miguel MJ, Albert D, Ferreira AC, Marín CM, Thiébaud M, Jacques I, Grayon M, Zygmunt MS, Garin-Bastuji B, Blasco JM, Sá MI.

Vet Microbiol. 2006 Jun 15;115(1-3):269-77. Epub 2006 Mar 10.


Characterisation of the genetic diversity of Brucella by multilocus sequencing.

Whatmore AM, Perrett LL, MacMillan AP.

BMC Microbiol. 2007 Apr 20;7:34.


Whole genome sequencing.

Ng PC, Kirkness EF.

Methods Mol Biol. 2010;628:215-26. doi: 10.1007/978-1-60327-367-1_12. Review.


Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Kisand V, Lettieri T.

BMC Genomics. 2013 Apr 1;14:211. doi: 10.1186/1471-2164-14-211.


Genome sequences of three live attenuated vaccine strains of Brucella species and implications for pathogenesis and differential diagnosis.

Wang Y, Ke Y, Wang Z, Yuan X, Qiu Y, Zhen Q, Xu J, Li T, Wang D, Huang L, Chen Z.

J Bacteriol. 2012 Nov;194(21):6012-3. doi: 10.1128/JB.01483-12.

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