Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 285

Related Citations for PubMed (Select 21486487)

1.

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.

2.

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.

3.

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.

4.

Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

Umemura M, Koyama Y, Takeda I, Hagiwara H, Ikegami T, Koike H, Machida M.

PLoS One. 2013 May 7;8(5):e63673. doi: 10.1371/journal.pone.0063673. Print 2013.

5.

Assembler for de novo assembly of large genomes.

Chu TC, Lu CH, Liu T, Lee GC, Li WH, Shih AC.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3417-24. doi: 10.1073/pnas.1314090110. Epub 2013 Aug 21.

6.

ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA.

Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266.

7.

Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.

8.

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Desai A, Marwah VS, Yadav A, Jha V, Dhaygude K, Bangar U, Kulkarni V, Jere A.

PLoS One. 2013 Apr 12;8(4):e60204. doi: 10.1371/journal.pone.0060204. Print 2013.

9.

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.

10.

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.

11.

GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.

12.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Kisand V, Lettieri T.

BMC Genomics. 2013 Apr 1;14:211. doi: 10.1186/1471-2164-14-211.

13.

Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.

Liu T, Tsai CH, Lee WB, Chiang JH.

PLoS One. 2013 Jul 29;8(7):e69503. doi: 10.1371/journal.pone.0069503. Print 2013.

14.

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.

15.

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.

16.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

17.

De novo likelihood-based measures for comparing genome assemblies.

Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M.

BMC Res Notes. 2013 Aug 22;6:334. doi: 10.1186/1756-0500-6-334.

18.

Whole-genome sequencing and assembly with high-throughput, short-read technologies.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S.

PLoS One. 2007 May 30;2(5):e484.

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.

Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome.

Wang Y, Yu Y, Pan B, Hao P, Li Y, Shao Z, Xu X, Li X.

BMC Syst Biol. 2012;6 Suppl 3:S21. doi: 10.1186/1752-0509-6-S3-S21. Epub 2012 Dec 17.

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk