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Items: 1 to 20 of 90

1.

Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.

Ramos RT, Carneiro AR, Caracciolo PH, Azevedo V, Schneider MP, Barh D, Silva A.

Bioinformation. 2013 Jun 29;9(11):599-604. doi: 10.6026/97320630009599. Print 2013.

2.

Simplifier: a web tool to eliminate redundant NGS contigs.

Ramos RT, Carneiro AR, Azevedo V, Schneider MP, Barh D, Silva A.

Bioinformation. 2012;8(20):996-9. doi: 10.6026/97320630008996. Epub 2012 Oct 13.

3.

CAR: contig assembly of prokaryotic draft genomes using rearrangements.

Lu CL, Chen KT, Huang SY, Chiu HT.

BMC Bioinformatics. 2014 Nov 28;15:381. doi: 10.1186/s12859-014-0381-3.

4.

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing.

Eastman AW, Yuan ZC.

Front Microbiol. 2015 Jan 21;5:769. doi: 10.3389/fmicb.2014.00769. eCollection 2014.

5.

Tracembler--software for in-silico chromosome walking in unassembled genomes.

Dong Q, Wilkerson MD, Brendel V.

BMC Bioinformatics. 2007 May 9;8:151.

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. Epub 2010 Dec 12.

PMID:
21149342
7.

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

Mariano DC, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HC, Silva A, Ramos RT, Azevedo VA.

BMC Bioinformatics. 2016 Dec 15;17(Suppl 18):456. doi: 10.1186/s12859-016-1344-7.

8.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes.

Dias Z, Dias U, Setubal JC.

BMC Bioinformatics. 2012 May 14;13:96. doi: 10.1186/1471-2105-13-96.

9.

Multi-CAR: a tool of contig scaffolding using multiple references.

Chen KT, Chen CJ, Shen HT, Liu CL, Huang SH, Lu CL.

BMC Bioinformatics. 2016 Dec 23;17(Suppl 17):469. doi: 10.1186/s12859-016-1328-7.

10.

GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

de Sá PH, Miranda F, Veras A, de Melo DM, Soares S, Pinheiro K, Guimarães L, Azevedo V, Silva A, Ramos RT.

PLoS One. 2016 May 12;11(5):e0155327. doi: 10.1371/journal.pone.0155327. eCollection 2016.

11.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.

Boisvert S, Laviolette F, Corbeil J.

J Comput Biol. 2010 Nov;17(11):1519-33. doi: 10.1089/cmb.2009.0238. Epub 2010 Oct 20.

12.

Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology.

Shaik S, Kumar N, Lankapalli AK, Tiwari SK, Baddam R, Ahmed N.

PLoS One. 2016 Jun 1;11(6):e0155459. doi: 10.1371/journal.pone.0155459. eCollection 2016.

13.

FGAP: an automated gap closing tool.

Piro VC, Faoro H, Weiss VA, Steffens MB, Pedrosa FO, Souza EM, Raittz RT.

BMC Res Notes. 2014 Jun 18;7:371. doi: 10.1186/1756-0500-7-371.

14.

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.

15.

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes.

Galardini M, Biondi EG, Bazzicalupo M, Mengoni A.

Source Code Biol Med. 2011 Jun 21;6:11. doi: 10.1186/1751-0473-6-11.

16.

GFinisher: a new strategy to refine and finish bacterial genome assemblies.

Guizelini D, Raittz RT, Cruz LM, Souza EM, Steffens MB, Pedrosa FO.

Sci Rep. 2016 Oct 10;6:34963. doi: 10.1038/srep34963.

17.

Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C.

Bioinformatics. 2015 Jun 15;31(12):i80-8. doi: 10.1093/bioinformatics/btv262.

18.

DraGnET: software for storing, managing and analyzing annotated draft genome sequence data.

Duncan S, Sirkanungo R, Miller L, Phillips GJ.

BMC Bioinformatics. 2010 Feb 22;11:100. doi: 10.1186/1471-2105-11-100.

19.

Mapping contigs using CONTIGuator.

Galardini M, Mengoni A, Bazzicalupo M.

Methods Mol Biol. 2015;1231:163-76. doi: 10.1007/978-1-4939-1720-4_11.

PMID:
25343865
20.

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.

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