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Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.

Cerdeira LT, Carneiro AR, Ramos RT, de Almeida SS, D'Afonseca V, Schneider MP, Baumbach J, Tauch A, McCulloch JA, Azevedo VA, Silva A.

J Microbiol Methods. 2011 Aug;86(2):218-23. doi: 10.1016/j.mimet.2011.05.008. Epub 2011 May 18.


De novo assembly of short sequence reads.

Paszkiewicz K, Studholme DJ.

Brief Bioinform. 2010 Sep;11(5):457-72. doi: 10.1093/bib/bbq020. Epub 2010 Aug 19. 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.


Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis.

Silva A, Schneider MP, Cerdeira L, Barbosa MS, Ramos RT, Carneiro AR, Santos R, Lima M, D'Afonseca V, Almeida SS, Santos AR, Soares SC, Pinto AC, Ali A, Dorella FA, Rocha F, de Abreu VA, Trost E, Tauch A, Shpigel N, Miyoshi A, Azevedo V.

J Bacteriol. 2011 Jan;193(1):323-4. doi: 10.1128/JB.01211-10. Epub 2010 Oct 29.


Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome.

Everett MV, Grau ED, Seeb JE.

Mol Ecol Resour. 2011 Mar;11 Suppl 1:93-108. doi: 10.1111/j.1755-0998.2010.02969.x.


Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome.

Wang Y, Yu Y, Pan B, Hao P, Li Y, Shao Z, Xu X, Li X.

BMC Syst Biol. 2012;6 Suppl 3:S21. doi: 10.1186/1752-0509-6-S3-S21. Epub 2012 Dec 17.


High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly.

Ramos RT, Carneiro AR, de Castro Soares S, Barbosa S, Varuzza L, Orabona G, Tauch A, Azevedo V, Schneider MP, Silva A.

J Microbiol Methods. 2013 Dec;95(3):441-7. doi: 10.1016/j.mimet.2013.06.006. Epub 2013 Jun 21.


Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.

Ramos RT, Carneiro AR, Soares Sde C, dos Santos AR, Almeida S, Guimarães L, Figueira F, Barbosa E, Tauch A, Azevedo V, Silva A.

Microb Biotechnol. 2013 Mar;6(2):150-6. doi: 10.1111/1751-7915.12006. Epub 2012 Dec 2.


Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.

Dutilh BE, Huynen MA, Strous M.

Bioinformatics. 2009 Nov 1;25(21):2878-81. doi: 10.1093/bioinformatics/btp377. Epub 2009 Jun 19.


A pilot study for channel catfish whole genome sequencing and de novo assembly.

Jiang Y, Lu J, Peatman E, Kucuktas H, Liu S, Wang S, Sun F, Liu Z.

BMC Genomics. 2011 Dec 22;12:629. doi: 10.1186/1471-2164-12-629.


De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J.

Genome Res. 2008 May;18(5):802-9. doi: 10.1101/gr.072033.107. Epub 2008 Mar 10.


De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.

Farrer RA, Kemen E, Jones JD, Studholme DJ.

FEMS Microbiol Lett. 2009 Feb;291(1):103-11. doi: 10.1111/j.1574-6968.2008.01441.x. Epub 2008 Dec 9.


Next-generation sequencing technologies and fragment assembly algorithms.

Lee H, Tang H.

Methods Mol Biol. 2012;855:155-74. doi: 10.1007/978-1-61779-582-4_5. Review.


GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.


Parallelized short read assembly of large genomes using de Bruijn graphs.

Liu Y, Schmidt B, Maskell DL.

BMC Bioinformatics. 2011 Aug 25;12:354. doi: 10.1186/1471-2105-12-354.


A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes.

Haridas S, Breuill C, Bohlmann J, Hsiang T.

J Microbiol Methods. 2011 Sep;86(3):368-75. doi: 10.1016/j.mimet.2011.06.019. Epub 2011 Jul 3.


A new strategy for better genome assembly from very short reads.

Ji Y, Shi Y, Ding G, Li Y.

BMC Bioinformatics. 2011 Dec 30;12:493. doi: 10.1186/1471-2105-12-493.


ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.


Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.


The present and future of de novo whole-genome assembly.

Sohn JI, Nam JW.

Brief Bioinform. 2016 Oct 14. pii: bbw096. [Epub ahead of print]


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