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FastUniq: a fast de novo duplicates removal tool for paired short reads.

Xu H, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S.

PLoS One. 2012;7(12):e52249. doi: 10.1371/journal.pone.0052249. Epub 2012 Dec 20.


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.


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.


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.


Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads.

Chong Z, Ruan J, Wu CI.

Bioinformatics. 2012 Nov 1;28(21):2732-7. doi: 10.1093/bioinformatics/bts482. Epub 2012 Sep 1.


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.


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.


SHRiMP: accurate mapping of short color-space reads.

Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.

PLoS Comput Biol. 2009 May;5(5):e1000386. doi: 10.1371/journal.pcbi.1000386. Epub 2009 May 22.


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.


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.


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.


Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.


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.


ConDeTri--a content dependent read trimmer for Illumina data.

Smeds L, Künstner A.

PLoS One. 2011;6(10):e26314. doi: 10.1371/journal.pone.0026314. Epub 2011 Oct 19.


Efficient alignment of pyrosequencing reads for re-sequencing applications.

Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT.

BMC Bioinformatics. 2011 May 16;12:163. doi: 10.1186/1471-2105-12-163.


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.


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.


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.


Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.


PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Chen Y, Souaiaia T, Chen T.

Bioinformatics. 2009 Oct 1;25(19):2514-21. doi: 10.1093/bioinformatics/btp486. Epub 2009 Aug 12.

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