Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 121

1.

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.

Zerbino DR, McEwen GK, Margulies EH, Birney E.

PLoS One. 2009 Dec 22;4(12):e8407. doi: 10.1371/journal.pone.0008407.

2.

SeqEntropy: genome-wide assessment of repeats for short read sequencing.

Chu HT, Hsiao WW, Tsao TT, Hsu DF, Chen CC, Lee SA, Kao CY.

PLoS One. 2013;8(3):e59484. doi: 10.1371/journal.pone.0059484. Epub 2013 Mar 27.

3.

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Genome Res. 2007 Nov;17(11):1697-706. Epub 2007 Oct 1.

4.

Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

Cahill MJ, Köser CU, Ross NE, Archer JA.

PLoS One. 2010 Jul 12;5(7):e11518. doi: 10.1371/journal.pone.0011518.

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.

PMID:
22492642
6.

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.

7.

QSRA: a quality-value guided de novo short read assembler.

Bryant DW Jr, Wong WK, Mockler TC.

BMC Bioinformatics. 2009 Feb 24;10:69. doi: 10.1186/1471-2105-10-69.

8.

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. Epub 2008 Dec 9.

9.
10.

Crystallizing short-read assemblies around seeds.

Hossain MS, Azimi N, Skiena S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16. doi: 10.1186/1471-2105-10-S1-S16.

11.

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. Epub 2009 Feb 27.

12.

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.

Wetzel J, Kingsford C, Pop M.

BMC Bioinformatics. 2011 Apr 13;12:95. doi: 10.1186/1471-2105-12-95.

13.

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

Palmer LE, Dejori M, Bolanos R, Fasulo D.

BMC Bioinformatics. 2010 Jan 15;11:33. doi: 10.1186/1471-2105-11-33.

14.

A pilot study for channel catfish whole genome sequencing and de novo assembly.

Jiang Y, Lu J, Peatman E, Kucuktas H, Liu S, Wang S, Sun F, Liu Z.

BMC Genomics. 2011 Dec 22;12:629. doi: 10.1186/1471-2164-12-629.

15.

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.

16.

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.

17.

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.

18.

PERGA: a paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach.

Zhu X, Leung HC, Chin FY, Yiu SM, Quan G, Liu B, Wang Y.

PLoS One. 2014 Dec 2;9(12):e114253. doi: 10.1371/journal.pone.0114253. eCollection 2014.

19.

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.

20.

EPGA: de novo assembly using the distributions of reads and insert size.

Luo J, Wang J, Zhang Z, Wu FX, Li M, Pan Y.

Bioinformatics. 2015 Mar 15;31(6):825-33. doi: 10.1093/bioinformatics/btu762. Epub 2014 Nov 17.

PMID:
25406329

Supplemental Content

Support Center