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Results: 1 to 20 of 125

Similar articles for PubMed (Select 21876754)

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. Epub 2011 Aug 18.

2.

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. Print 2013.

3.

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. Print 2013.

4.

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. Epub 2008 Mar 13.

5.

Evaluation of short read metagenomic assembly.

Charuvaka A, Rangwala H.

BMC Genomics. 2011;12 Suppl 2:S8. doi: 10.1186/1471-2164-12-S2-S8. Epub 2011 Jul 27.

6.

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. Epub 2011 Oct 14.

7.

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. Epub 2007 Oct 1.

8.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Dayarian A, Michael TP, Sengupta AM.

BMC Bioinformatics. 2010 Jun 24;11:345. doi: 10.1186/1471-2105-11-345.

9.

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.

10.

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.

Bao E, Jiang T, Girke T.

Bioinformatics. 2014 Jun 15;30(12):i319-i328. doi: 10.1093/bioinformatics/btu291.

11.

Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.

12.

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.

13.

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson MJ, Brinza D, Pevzner PA.

Genome Res. 2009 Feb;19(2):336-46. doi: 10.1101/gr.079053.108. Epub 2008 Dec 3.

14.

Local de novo assembly of RAD paired-end contigs using short sequencing reads.

Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA.

PLoS One. 2011 Apr 13;6(4):e18561. doi: 10.1371/journal.pone.0018561.

15.

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. eCollection 2014.

16.

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. Epub 2010 Dec 12.

17.

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. Epub 2014 Jun 11.

PMID:
24919879
18.

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. Epub 2012 Aug 14.

19.

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome.

Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ.

BMC Genomics. 2013 Oct 1;14:670. doi: 10.1186/1471-2164-14-670.

20.

Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT, Durbin R.

Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111. Epub 2011 Dec 7.

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