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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.


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.


Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT, Durbin R.

Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111. Epub 2011 Dec 7.


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.


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.


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.


Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

Peterlongo P, Chikhi R.

BMC Bioinformatics. 2012 Mar 23;13:48. doi: 10.1186/1471-2105-13-48.


A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.

Bioinformatics. 2009 May 1;25(9):1118-24. doi: 10.1093/bioinformatics/btp131. Epub 2009 Mar 5.


A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework.

Chang YJ, Chen CC, Chen CL, Ho JM.

BMC Genomics. 2012;13 Suppl 7:S28. doi: 10.1186/1471-2164-13-S7-S28. Epub 2012 Dec 13.


Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.


Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.


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.


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.


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.


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.


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.


Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons.

Vezzi F, Narzisi G, Mishra B.

PLoS One. 2012;7(12):e52210. doi: 10.1371/journal.pone.0052210. Epub 2012 Dec 28.


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.


Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 3.


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.

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