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Items: 1 to 20 of 422

1.

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.

Kundeti VK, Rajasekaran S, Dinh H, Vaughn M, Thapar V.

BMC Bioinformatics. 2010 Nov 15;11:560. doi: 10.1186/1471-2105-11-560.

2.

AN EFFICIENT ALGORITHM FOR CHINESE POSTMAN WALK ON BI-DIRECTED DE BRUIJN GRAPHS.

Kundeti V, Rajasekaran S, Dinh H.

Discrete Math Algorithms Appl. 2010;1:184-196.

3.

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.

Shariat B, Movahedi NS, Chitsaz H, Boucher C.

BMC Genomics. 2014;15 Suppl 10:S9. doi: 10.1186/1471-2164-15-S10-S9. Epub 2014 Dec 12.

4.

Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches.

Cherukuri Y, Janga SC.

BMC Genomics. 2016 Aug 22;17 Suppl 7:507. doi: 10.1186/s12864-016-2895-8.

5.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.

6.

Read mapping on de Bruijn graphs.

Limasset A, Cazaux B, Rivals E, Peterlongo P.

BMC Bioinformatics. 2016 Jun 16;17(1):237. doi: 10.1186/s12859-016-1103-9.

7.

Efficient construction of an assembly string graph using the FM-index.

Simpson JT, Durbin R.

Bioinformatics. 2010 Jun 15;26(12):i367-73. doi: 10.1093/bioinformatics/btq217.

8.

An efficient algorithm for DNA fragment assembly in MapReduce.

Xu B, Gao J, Li C.

Biochem Biophys Res Commun. 2012 Sep 28;426(3):395-8. doi: 10.1016/j.bbrc.2012.08.101. Epub 2012 Aug 29.

PMID:
22960169
9.

Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform.

Baier U, Beller T, Ohlebusch E.

Bioinformatics. 2016 Feb 15;32(4):497-504. doi: 10.1093/bioinformatics/btv603. Epub 2015 Oct 26.

PMID:
26504144
10.

A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data.

Sze SH, Tarone AM.

BMC Genomics. 2014;15 Suppl 5:S6. doi: 10.1186/1471-2164-15-S5-S6. Epub 2014 Jul 14.

11.

Compacting de Bruijn graphs from sequencing data quickly and in low memory.

Chikhi R, Limasset A, Medvedev P.

Bioinformatics. 2016 Jun 15;32(12):i201-i208. doi: 10.1093/bioinformatics/btw279.

12.

A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly.

Dinh H, Rajasekaran S.

Bioinformatics. 2011 Jul 15;27(14):1901-7. doi: 10.1093/bioinformatics/btr321. Epub 2011 Jun 2.

13.

Compact representation of k-mer de Bruijn graphs for genome read assembly.

Rødland EA.

BMC Bioinformatics. 2013 Oct 23;14:313. doi: 10.1186/1471-2105-14-313.

14.

The fragment assembly string graph.

Myers EW.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii79-85.

PMID:
16204131
15.

Integration of string and de Bruijn graphs for genome assembly.

Huang YT, Liao CF.

Bioinformatics. 2016 May 1;32(9):1301-7. doi: 10.1093/bioinformatics/btw011. Epub 2016 Jan 10.

PMID:
26755626
16.

String graph construction using incremental hashing.

Ben-Bassat I, Chor B.

Bioinformatics. 2014 Dec 15;30(24):3515-23. doi: 10.1093/bioinformatics/btu578. Epub 2014 Sep 2.

PMID:
25183486
17.

FastEtch: A Fast Sketch-based Assembler for Genomes.

Ghosh P, Kalyanaraman A.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep 11. doi: 10.1109/TCBB.2017.2737999. [Epub ahead of print]

PMID:
28910776
18.

On the representation of de Bruijn graphs.

Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P.

J Comput Biol. 2015 May;22(5):336-52. doi: 10.1089/cmb.2014.0160. Epub 2015 Jan 28.

PMID:
25629448
19.

The present and future of de novo whole-genome assembly.

Sohn JI, Nam JW.

Brief Bioinform. 2016 Oct 14. pii: bbw096. [Epub ahead of print]

PMID:
27742661
20.

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Gonnella G, Kurtz S.

BMC Bioinformatics. 2012 May 6;13:82. doi: 10.1186/1471-2105-13-82.

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