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De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.

Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR, Barrett CL.

PLoS One. 2010 Jun 8;5(6):e10922. doi: 10.1371/journal.pone.0010922.


Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Desai A, Marwah VS, Yadav A, Jha V, Dhaygude K, Bangar U, Kulkarni V, Jere A.

PLoS One. 2013 Apr 12;8(4):e60204. doi: 10.1371/journal.pone.0060204.


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 assembly of short sequence reads.

Paszkiewicz K, Studholme DJ.

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


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.


When is a microbial culture "pure"? Persistent cryptic contaminant escapes detection even with deep genome sequencing.

Shrestha PM, Nevin KP, Shrestha M, Lovley DR.

MBio. 2013 Mar 12;4(2):e00591-12. doi: 10.1128/mBio.00591-12.


De novo sequencing of plant genomes using second-generation technologies.

Imelfort M, Edwards D.

Brief Bioinform. 2009 Nov;10(6):609-18. doi: 10.1093/bib/bbp039. Review.


Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30.


An integrated pipeline for de novo assembly of microbial genomes.

Tritt A, Eisen JA, Facciotti MT, Darling AE.

PLoS One. 2012;7(9):e42304. doi: 10.1371/journal.pone.0042304.


Using Illumina next generation sequencing technologies to sequence multigene families in de novo species.

Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC.

Mol Ecol Resour. 2013 May;13(3):510-21. doi: 10.1111/1755-0998.12087.


De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M.

PLoS Genet. 2010 Apr 8;6(4):e1000891. doi: 10.1371/journal.pgen.1000891.


Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.

Kim BC, Postier BL, Didonato RJ, Chaudhuri SK, Nevin KP, Lovley DR.

Bioelectrochemistry. 2008 Jun;73(1):70-5. doi: 10.1016/j.bioelechem.2008.04.023. Erratum in: Bioelectrochemistry. 2008 Nov;74(1):222.


Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.

Haiminen N, Kuhn DN, Parida L, Rigoutsos I.

PLoS One. 2011;6(9):e24182. doi: 10.1371/journal.pone.0024182. Erratum in: PLoS One. 2011:6(10). doi: 10.1371/annotation/bb125f93-80d3-4dd1-adfe-03d9fb740f3b. PLoS One. 2011;6(10). doi: 10.1371/annotation/176d83be-ed67-4205-9265-7208792d3dcf.


GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D.

Bioinformatics. 2012 Jun 1;28(11):1429-37. doi: 10.1093/bioinformatics/bts175.


Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.

Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S.

Brief Bioinform. 2012 May;13(3):269-80. doi: 10.1093/bib/bbr063. Review.


Correction of sequencing errors in a mixed set of reads.

Salmela L.

Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151.


454 sequencing put to the test using the complex genome of barley.

Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N.

BMC Genomics. 2006 Oct 26;7:275.


Optimal algorithms for haplotype assembly from whole-genome sequence data.

He D, Choi A, Pipatsrisawat K, Darwiche A, Eskin E.

Bioinformatics. 2010 Jun 15;26(12):i183-90. doi: 10.1093/bioinformatics/btq215.

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