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Items: 1 to 20 of 184

1.

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.

2.

SEED: efficient clustering of next-generation sequences.

Bao E, Jiang T, Kaloshian I, Girke T.

Bioinformatics. 2011 Sep 15;27(18):2502-9. doi: 10.1093/bioinformatics/btr447.

3.

Paired-end RAD-seq for de novo assembly and marker design without available reference.

Willing EM, Hoffmann M, Klein JD, Weigel D, Dreyer C.

Bioinformatics. 2011 Aug 15;27(16):2187-93. doi: 10.1093/bioinformatics/btr346.

4.

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.

Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W.

Bioinformatics. 2011 Jul 15;27(14):1922-8. doi: 10.1093/bioinformatics/btr310.

5.

CLASS: constrained transcript assembly of RNA-seq reads.

Song L, Florea L.

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14.

6.

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.

7.

EasyCluster2: an improved tool for clustering and assembling long transcriptome reads.

Bevilacqua V, Pietroleonardo N, Giannino E, Stroppa F, Simone D, Pesole G, Picardi E.

BMC Bioinformatics. 2014;15 Suppl 15:S7. doi: 10.1186/1471-2105-15-S15-S7.

8.

SlideSort: all pairs similarity search for short reads.

Shimizu K, Tsuda K.

Bioinformatics. 2011 Feb 15;27(4):464-70. doi: 10.1093/bioinformatics/btq677.

9.

Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

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

10.

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.

11.

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.

12.

Local de novo assembly of RAD paired-end contigs using short sequencing reads.

Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA.

PLoS One. 2011 Apr 13;6(4):e18561. doi: 10.1371/journal.pone.0018561.

13.

Population genomic analysis of model and nonmodel organisms using sequenced RAD tags.

Hohenlohe PA, Catchen J, Cresko WA.

Methods Mol Biol. 2012;888:235-60. doi: 10.1007/978-1-61779-870-2_14.

PMID:
22665285
14.

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.

15.

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.

16.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, R├Ątsch G.

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

17.
18.

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.

19.

Correction of sequencing errors in a mixed set of reads.

Salmela L.

Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151.

20.

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.

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