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COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.

Liu B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R.

Bioinformatics. 2012 Nov 15;28(22):2870-4. doi: 10.1093/bioinformatics/bts563. Epub 2012 Oct 8.


FLASH: fast length adjustment of short reads to improve genome assemblies.

Magoč T, Salzberg SL.

Bioinformatics. 2011 Nov 1;27(21):2957-63. doi: 10.1093/bioinformatics/btr507. Epub 2011 Sep 7.


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.


pIRS: Profile-based Illumina pair-end reads simulator.

Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W.

Bioinformatics. 2012 Jun 1;28(11):1533-5. doi: 10.1093/bioinformatics/bts187. Epub 2012 Apr 15.


ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.

Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.

Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169. Epub 2013 Apr 19.


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.


Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

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


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.


QuorUM: An Error Corrector for Illumina Reads.

Marçais G, Yorke JA, Zimin A.

PLoS One. 2015 Jun 17;10(6):e0130821. doi: 10.1371/journal.pone.0130821. eCollection 2015.


Blue: correcting sequencing errors using consensus and context.

Greenfield P, Duesing K, Papanicolaou A, Bauer DC.

Bioinformatics. 2014 Oct;30(19):2723-32. doi: 10.1093/bioinformatics/btu368. Epub 2014 Jun 11.


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.


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.


Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

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


The MaSuRCA genome assembler.

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.

Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476. Epub 2013 Aug 29.


Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.

Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI.

BMC Genomics. 2013 Oct 17;14:711. doi: 10.1186/1471-2164-14-711.


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.


Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, Rätsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.


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.


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.


Evaluation of short read metagenomic assembly.

Charuvaka A, Rangwala H.

BMC Genomics. 2011;12 Suppl 2:S8. doi: 10.1186/1471-2164-12-S2-S8. Epub 2011 Jul 27.

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