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Items: 1 to 20 of 95

1.

Visualization and quality assessment of de novo genome assemblies.

Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.

Bioinformatics. 2011 Dec 15;27(24):3425-6. doi: 10.1093/bioinformatics/btr569.

PMID:
21994228
2.

Bandage: interactive visualization of de novo genome assemblies.

Wick RR, Schultz MB, Zobel J, Holt KE.

Bioinformatics. 2015 Oct 15;31(20):3350-2. doi: 10.1093/bioinformatics/btv383.

3.

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
4.

Paired-end RAD-seq for de novo assembly and marker design without available reference.

Willing EM, Hoffmann M, Klein JD, Weigel D, Dreyer C.

Bioinformatics. 2011 Aug 15;27(16):2187-93. doi: 10.1093/bioinformatics/btr346.

PMID:
21712251
5.

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
6.

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.

7.

OSLay: optimal syntenic layout of unfinished assemblies.

Richter DC, Schuster SC, Huson DH.

Bioinformatics. 2007 Jul 1;23(13):1573-9.

PMID:
17463020
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.

9.

Ragout-a reference-assisted assembly tool for bacterial genomes.

Kolmogorov M, Raney B, Paten B, Pham S.

Bioinformatics. 2014 Jun 15;30(12):i302-9. doi: 10.1093/bioinformatics/btu280.

10.

A distributed environment for physical map construction.

Grigoriev A, Levin A, Lehrach H.

Bioinformatics. 1998;14(3):252-8.

PMID:
9614268
11.

Finishing bacterial genome assemblies with Mix.

Soueidan H, Maurier F, Groppi A, Sirand-Pugnet P, Tardy F, Citti C, Dupuy V, Nikolski M.

BMC Bioinformatics. 2013;14 Suppl 15:S16. doi: 10.1186/1471-2105-14-S15-S16.

12.

Improved gap size estimation for scaffolding algorithms.

Sahlin K, Street N, Lundeberg J, Arvestad L.

Bioinformatics. 2012 Sep 1;28(17):2215-22.

PMID:
22923455
13.

Assembly reconciliation.

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

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

PMID:
18057021
14.

BFC: correcting Illumina sequencing errors.

Li H.

Bioinformatics. 2015 Sep 1;31(17):2885-7. doi: 10.1093/bioinformatics/btv290.

15.

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD.

Bioinformatics. 2014 Oct;30(19):2709-16. doi: 10.1093/bioinformatics/btu391.

16.

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.

Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.

Bioinformatics. 2012 Apr 1;28(7):1024-5. doi: 10.1093/bioinformatics/bts064.

PMID:
22302574
17.

preAssemble: a tool for automatic sequencer trace data processing.

Adzhubei AA, Laerdahl JK, Vlasova AV.

BMC Bioinformatics. 2006 Jan 17;7:22.

18.

QUAST: quality assessment tool for genome assemblies.

Gurevich A, Saveliev V, Vyahhi N, Tesler G.

Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086.

19.

Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation.

Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, Howard JJ, Ballesteros E, Gupta S, Widger W, Fofanov Y.

BMC Bioinformatics. 2012 Jul 16;13:166. doi: 10.1186/1471-2105-13-166.

20.

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.

PMID:
20724458

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