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Items: 1 to 20 of 63

1.

A fast hybrid short read fragment assembly algorithm.

Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ.

Bioinformatics. 2009 Sep 1;25(17):2279-80. doi: 10.1093/bioinformatics/btp374. Epub 2009 Jun 17.

PMID:
19535537
2.

SHREC: a short-read error correction method.

Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B.

Bioinformatics. 2009 Sep 1;25(17):2157-63. doi: 10.1093/bioinformatics/btp379. Epub 2009 Jun 19.

PMID:
19542152
3.

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.

4.

A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware.

Shi H, Schmidt B, Liu W, Müller-Wittig W.

J Comput Biol. 2010 Apr;17(4):603-15. doi: 10.1089/cmb.2009.0062.

PMID:
20426693
5.

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.

6.

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads.

Warnke JD, Ali HH.

BMC Bioinformatics. 2013;14 Suppl 11:S7. doi: 10.1186/1471-2105-14-S11-S7. Epub 2013 Nov 4.

7.

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.

8.

Gossamer--a resource-efficient de novo assembler.

Conway T, Wazny J, Bromage A, Zobel J, Beresford-Smith B.

Bioinformatics. 2012 Jul 15;28(14):1937-8. doi: 10.1093/bioinformatics/bts297. Epub 2012 May 18.

PMID:
22611131
9.

Parallelized short read assembly of large genomes using de Bruijn graphs.

Liu Y, Schmidt B, Maskell DL.

BMC Bioinformatics. 2011 Aug 25;12:354. doi: 10.1186/1471-2105-12-354.

10.

SeedsGraph: an efficient assembler for next-generation sequencing data.

Wang C, Guo M, Liu X, Liu Y, Zou Q.

BMC Med Genomics. 2015;8 Suppl 2:S13. doi: 10.1186/1755-8794-8-S2-S13. Epub 2015 May 29.

11.

Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.

12.

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.

Li Z, Chen Y, Mu D, Yuan J, Shi Y, Zhang H, Gan J, Li N, Hu X, Liu B, Yang B, Fan W.

Brief Funct Genomics. 2012 Jan;11(1):25-37. doi: 10.1093/bfgp/elr035. Epub 2011 Dec 19. Review.

PMID:
22184334
13.

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
14.

Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

Bioinformatics. 2004 Sep 1;20(13):2067-74. Epub 2004 Apr 1.

PMID:
15059830
15.

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.

Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, Østerås M, François P, Schrenzel J.

Bioinformatics. 2014 Jan 1;30(1):40-9. doi: 10.1093/bioinformatics/btt590. Epub 2013 Oct 15.

PMID:
24130309
16.

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.

17.

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.

Cerdeira LT, Carneiro AR, Ramos RT, de Almeida SS, D'Afonseca V, Schneider MP, Baumbach J, Tauch A, McCulloch JA, Azevedo VA, Silva A.

J Microbiol Methods. 2011 Aug;86(2):218-23. doi: 10.1016/j.mimet.2011.05.008. Epub 2011 May 18.

18.

De novo assembly of short sequence reads.

Paszkiewicz K, Studholme DJ.

Brief Bioinform. 2010 Sep;11(5):457-72. doi: 10.1093/bib/bbq020. Epub 2010 Aug 19. Review.

PMID:
20724458
19.

Next-generation sequencing technologies and fragment assembly algorithms.

Lee H, Tang H.

Methods Mol Biol. 2012;855:155-74. doi: 10.1007/978-1-61779-582-4_5. Review.

PMID:
22407708
20.

EDAR: an efficient error detection and removal algorithm for next generation sequencing data.

Zhao X, Palmer LE, Bolanos R, Mircean C, Fasulo D, Wittenberg GM.

J Comput Biol. 2010 Nov;17(11):1549-60. doi: 10.1089/cmb.2010.0127. Epub 2010 Oct 25.

PMID:
20973743

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