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Items: 1 to 20 of 115

1.

Meraculous: de novo genome assembly with short paired-end reads.

Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS.

PLoS One. 2011;6(8):e23501. doi: 10.1371/journal.pone.0023501.

2.

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Genome Res. 2007 Nov;17(11):1697-706.

3.

Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

Umemura M, Koyama Y, Takeda I, Hagiwara H, Ikegami T, Koike H, Machida M.

PLoS One. 2013 May 7;8(5):e63673. doi: 10.1371/journal.pone.0063673.

4.

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404. doi: 10.1186/1471-2164-9-404.

5.

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.

6.

Scaffolding pre-assembled contigs using SSPACE.

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W.

Bioinformatics. 2011 Feb 15;27(4):578-9. doi: 10.1093/bioinformatics/btq683.

PMID:
21149342
7.

Blue: correcting sequencing errors using consensus and context.

Greenfield P, Duesing K, Papanicolaou A, Bauer DC.

Bioinformatics. 2014 Oct;30(19):2723-32. doi: 10.1093/bioinformatics/btu368.

PMID:
24919879
8.

The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK, Wang J, Deyholos MK.

Plant J. 2012 Nov;72(3):461-73. doi: 10.1111/j.1365-313X.2012.05093.x.

9.

PE-Assembler: de novo assembler using short paired-end reads.

Ariyaratne PN, Sung WK.

Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626.

PMID:
21149345
10.

ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.

Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.

Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169.

PMID:
23603334
11.

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

Palmer LE, Dejori M, Bolanos R, Fasulo D.

BMC Bioinformatics. 2010 Jan 15;11:33. doi: 10.1186/1471-2105-11-33.

12.

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach.

Zhu X, Leung HC, Chin FY, Yiu SM, Quan G, Liu B, Wang Y.

PLoS One. 2014 Dec 2;9(12):e114253. doi: 10.1371/journal.pone.0114253.

13.

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.

14.

The complex task of choosing a de novo assembly: lessons from fungal genomes.

Gallo JE, Muñoz JF, Misas E, McEwen JG, Clay OK.

Comput Biol Chem. 2014 Dec;53 Pt A:97-107. doi: 10.1016/j.compbiolchem.2014.08.014.

PMID:
25262360
15.

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.

Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P.

J Comput Biol. 2011 Nov;18(11):1625-34. doi: 10.1089/cmb.2011.0151.

16.

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.

17.

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.

18.

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.

PMID:
22492642
19.

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):810-20. doi: 10.1101/gr.7337908.

20.

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.

Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI.

BMC Genomics. 2013 Oct 17;14:711. doi: 10.1186/1471-2164-14-711.

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