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Results: 1 to 20 of 174

1.

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.

Tsai IJ, Otto TD, Berriman M.

Genome Biol. 2010;11(4):R41. doi: 10.1186/gb-2010-11-4-r41. Epub 2010 Apr 13.

PMID:
20388197
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.

Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P.

BMC Genomics. 2008 Dec 16;9:603. doi: 10.1186/1471-2164-9-603.

PMID:
19087275
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Assembly reconciliation.

Zimin AV, Smith DR, Sutton G, Yorke JA.

Bioinformatics. 2008 Jan 1;24(1):42-5. Epub 2007 Dec 5.

PMID:
18057021
[PubMed - indexed for MEDLINE]
Free Article
4.

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.

PMID:
20724458
[PubMed - indexed for MEDLINE]
Free Article
5.

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.

van Hijum SA, Zomer AL, Kuipers OP, Kok J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W560-6.

PMID:
15980536
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

Bioinformatics. 2004 Sep 1;20(13):2067-74. Epub 2004 Apr 1.

PMID:
15059830
[PubMed - indexed for MEDLINE]
Free Article
7.

Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.

PMID:
18083777
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.

English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA.

PLoS One. 2012;7(11):e47768. doi: 10.1371/journal.pone.0047768. Epub 2012 Nov 21.

PMID:
23185243
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22208765
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
19251739
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.

Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJ.

Genome Biol. 2009;10(9):R94. doi: 10.1186/gb-2009-10-9-r94. Epub 2009 Sep 11.

PMID:
19747388
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
17908823
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An ORFome assembly approach to metagenomics sequences analysis.

Ye Y, Tang H.

Comput Syst Bioinformatics Conf. 2008;7:3-13.

PMID:
19642264
[PubMed - indexed for MEDLINE]
Free Article
14.

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD.

Nat Protoc. 2012 Jun 7;7(7):1260-84. doi: 10.1038/nprot.2012.068.

PMID:
22678431
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Integrating sequence with FPC fingerprint maps.

Nelson W, Soderlund C.

Nucleic Acids Res. 2009 Apr;37(5):e36. doi: 10.1093/nar/gkp034. Epub 2009 Jan 30.

PMID:
19181701
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
21149342
[PubMed - indexed for MEDLINE]
Free Article
17.

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. Epub 2012 Apr 6.

PMID:
22492642
[PubMed - indexed for MEDLINE]
Free Article
18.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. doi: 10.1073/pnas.1017351108. Epub 2010 Dec 27.

PMID:
21187386
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A tool for analyzing mate pairs in assemblies (TAMPA).

Dew IM, Walenz B, Sutton G.

J Comput Biol. 2005 Jun;12(5):497-513.

PMID:
15952874
[PubMed - indexed for MEDLINE]
20.

EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome.

Jain M, Shrager J, Harris EH, Halbrook R, Grossman AR, Hauser C, Vallon O.

Nucleic Acids Res. 2007;35(6):2074-83. Epub 2007 Mar 13.

PMID:
17355987
[PubMed - indexed for MEDLINE]
Free PMC Article

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