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Results: 1 to 20 of 80

1.

Assisted assembly: how to improve a de novo genome assembly by using related species.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB.

Genome Biol. 2009;10(8):R88. doi: 10.1186/gb-2009-10-8-r88. Epub 2009 Aug 27.

PMID:
19712469
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Correcting short reads with high error rates for improved sequencing result.

Wong TK, Lam TW, Chan PY, Yiu SM.

Int J Bioinform Res Appl. 2009;5(2):224-37.

PMID:
19324607
[PubMed - indexed for MEDLINE]
3.

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.

Li H.

Bioinformatics. 2012 Jul 15;28(14):1838-44. doi: 10.1093/bioinformatics/bts280. Epub 2012 May 7.

PMID:
22569178
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Calling SNPs without a reference sequence.

Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W.

BMC Bioinformatics. 2010 Mar 15;11:130. doi: 10.1186/1471-2105-11-130.

PMID:
20230626
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Correcting base-assignment errors in repeat regions of shotgun assembly.

Zhi D, Keich U, Pevzner P, Heber S, Tang H.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):54-64.

PMID:
17277413
[PubMed - indexed for MEDLINE]
6.

A preprocessor for shotgun assembly of large genomes.

Roberts M, Hunt BR, Yorke JA, Bolanos RA, Delcher AL.

J Comput Biol. 2004;11(4):734-52.

PMID:
15579242
[PubMed - indexed for MEDLINE]
7.

Application of a superword array in genome assembly.

Huang X, Yang SP, Chinwalla AT, Hillier LW, Minx P, Mardis ER, Wilson RK.

Nucleic Acids Res. 2006 Jan 5;34(1):201-5. Print 2006.

PMID:
16397298
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

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
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.

PMID:
19077061
[PubMed - indexed for MEDLINE]
11.

Parametric complexity of sequence assembly: theory and applications to next generation sequencing.

Nagarajan N, Pop M.

J Comput Biol. 2009 Jul;16(7):897-908. doi: 10.1089/cmb.2009.0005.

PMID:
19580519
[PubMed - indexed for MEDLINE]
12.

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]
13.

Computational methods for discovering structural variation with next-generation sequencing.

Medvedev P, Stanciu M, Brudno M.

Nat Methods. 2009 Nov;6(11 Suppl):S13-20. doi: 10.1038/nmeth.1374. Review.

PMID:
19844226
[PubMed - indexed for MEDLINE]
14.

QSRA: a quality-value guided de novo short read assembler.

Bryant DW Jr, Wong WK, Mockler TC.

BMC Bioinformatics. 2009 Feb 24;10:69. doi: 10.1186/1471-2105-10-69.

PMID:
19239711
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Whole genome assembly from 454 sequencing output via modified DNA graph concept.

Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt D, Przybytek J, Swiercz A, Szajkowski L.

Comput Biol Chem. 2009 Jun;33(3):224-30. doi: 10.1016/j.compbiolchem.2009.04.005. Epub 2009 May 3.

PMID:
19477687
[PubMed - indexed for MEDLINE]
16.

Gene prediction: compare and CONTRAST.

Flicek P.

Genome Biol. 2007;8(12):233. Review.

PMID:
18096089
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

PGA4genomics for comparative genome assembly based on genetic algorithm optimization.

Zhao F, Hou H, Bao Q, Wu J.

Genomics. 2009 Oct;94(4):284-6. doi: 10.1016/j.ygeno.2009.06.006. Epub 2009 Jun 30.

PMID:
19573591
[PubMed - indexed for MEDLINE]
Free Article
18.

Genome reassembly with high-throughput sequencing data.

Parrish N, Sudakov B, Eskin E.

BMC Genomics. 2013;14 Suppl 1:S8. doi: 10.1186/1471-2164-14-S1-S8. Epub 2013 Jan 21.

PMID:
23368744
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Barcodes for genomes and applications.

Zhou F, Olman V, Xu Y.

BMC Bioinformatics. 2008 Dec 17;9:546. doi: 10.1186/1471-2105-9-546.

PMID:
19091119
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Computational tools for the analysis of rearrangements in mammalian genomes.

Tesler G, Bourque G.

Methods Mol Biol. 2008;422:145-70. doi: 10.1007/978-1-59745-581-7_10.

PMID:
18629666
[PubMed - indexed for MEDLINE]

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