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Items: 1 to 20 of 157

1.

High-throughput genome scaffolding from in vivo DNA interaction frequency.

Kaplan N, Dekker J.

Nat Biotechnol. 2013 Dec;31(12):1143-7. doi: 10.1038/nbt.2768. Epub 2013 Nov 24.

2.

Genomes in 3D improve one-dimensional assemblies.

Rusk N.

Nat Methods. 2014 Jan;11(1):5. No abstract available.

PMID:
24524125
3.

Genome assembly and haplotyping with Hi-C.

Korbel JO, Lee C.

Nat Biotechnol. 2013 Dec;31(12):1099-101. doi: 10.1038/nbt.2764. No abstract available.

PMID:
24316648
4.

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J.

Nat Biotechnol. 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.2727. Epub 2013 Nov 3.

5.

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.

6.

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
7.

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.

8.

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.

Bao E, Jiang T, Girke T.

Bioinformatics. 2014 Jun 15;30(12):i319-i328. doi: 10.1093/bioinformatics/btu291.

9.

ILP-based maximum likelihood genome scaffolding.

Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.

10.

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.

11.

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments.

Kosugi S, Hirakawa H, Tabata S.

Bioinformatics. 2015 Dec 1;31(23):3733-41. doi: 10.1093/bioinformatics/btv465. Epub 2015 Aug 10.

PMID:
26261222
12.

Graph accordance of next-generation sequence assemblies.

Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM.

Bioinformatics. 2012 Jan 1;28(1):13-6. doi: 10.1093/bioinformatics/btr588. Epub 2011 Oct 23.

13.

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
14.

A de novo metagenomic assembly program for shotgun DNA reads.

Lai B, Ding R, Li Y, Duan L, Zhu H.

Bioinformatics. 2012 Jun 1;28(11):1455-62. doi: 10.1093/bioinformatics/bts162. Epub 2012 Apr 11.

15.

Optimal assembly for high throughput shotgun sequencing.

Bresler G, Bresler M, Tse D.

BMC Bioinformatics. 2013;14 Suppl 5:S18. doi: 10.1186/1471-2105-14-S5-S18. Epub 2013 Jul 9.

16.

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.

17.

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.

18.

High-quality genome (re)assembly using chromosomal contact data.

Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R.

Nat Commun. 2014 Dec 17;5:5695. doi: 10.1038/ncomms6695.

19.

Efficient and scalable scaffolding using optical restriction maps.

Saha S, Rajasekaran S.

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

20.

Telescoper: de novo assembly of highly repetitive regions.

Bresler M, Sheehan S, Chan AH, Song YS.

Bioinformatics. 2012 Sep 15;28(18):i311-i317. doi: 10.1093/bioinformatics/bts399.

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