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Items: 1 to 20 of 111

1.

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Gao S, Sung WK, Nagarajan N.

J Comput Biol. 2011 Nov;18(11):1681-91. doi: 10.1089/cmb.2011.0170. Epub 2011 Sep 19.

2.

SCARPA: scaffolding reads with practical algorithms.

Donmez N, Brudno M.

Bioinformatics. 2013 Feb 15;29(4):428-34. doi: 10.1093/bioinformatics/bts716. Epub 2012 Dec 29.

PMID:
23274213
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. Epub 2012 Apr 6.

PMID:
22492642
4.

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.

5.

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.

Gao S, Bertrand D, Chia BK, Nagarajan N.

Genome Biol. 2016 May 11;17:102. doi: 10.1186/s13059-016-0951-y.

6.

ScaffMatch: scaffolding algorithm based on maximum weight matching.

Mandric I, Zelikovsky A.

Bioinformatics. 2015 Aug 15;31(16):2632-8. doi: 10.1093/bioinformatics/btv211. Epub 2015 Apr 17.

PMID:
25890305
7.

Heterozygous genome assembly via binary classification of homologous sequence.

Bodily PM, Fujimoto M, Ortega C, Okuda N, Price JC, Clement MJ, Snell Q.

BMC Bioinformatics. 2015;16 Suppl 7:S5. doi: 10.1186/1471-2105-16-S7-S5. Epub 2015 Apr 23.

8.

Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework.

Fang CH, Chang YJ, Chung WC, Hsieh PH, Lin CY, Ho JM.

BMC Genomics. 2015;16 Suppl 12:S9. doi: 10.1186/1471-2164-16-S12-S9. Epub 2015 Dec 9.

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.

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.

11.

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
12.

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly.

Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA.

J Comput Biol. 2013 Apr;20(4):359-71. doi: 10.1089/cmb.2012.0098. Epub 2012 Jul 17.

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.

A comprehensive evaluation of assembly scaffolding tools.

Hunt M, Newbold C, Berriman M, Otto TD.

Genome Biol. 2014 Mar 3;15(3):R42. doi: 10.1186/gb-2014-15-3-r42.

15.

SLIQ: simple linear inequalities for efficient contig scaffolding.

Roy RS, Chen KC, Sengupta AM, Schliep A.

J Comput Biol. 2012 Oct;19(10):1162-75. doi: 10.1089/cmb.2011.0263.

PMID:
23057825
16.

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.

17.

OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly.

Chen YM, Yu CH, Hwang CC, Liu T.

BMC Syst Biol. 2013;7 Suppl 6:S7. doi: 10.1186/1752-0509-7-S6-S7. Epub 2013 Dec 13.

18.

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.

19.

GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.

20.

MeDuSa: a multi-draft based scaffolder.

Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, LiĆ³ P, Crescenzi P, Fani R, Fondi M.

Bioinformatics. 2015 Aug 1;31(15):2443-51. doi: 10.1093/bioinformatics/btv171. Epub 2015 Mar 25.

PMID:
25810435

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