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Items: 1 to 20 of 84

1.

BRAT: bisulfite-treated reads analysis tool.

Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S.

Bioinformatics. 2010 Feb 15;26(4):572-3. doi: 10.1093/bioinformatics/btp706. Epub 2009 Dec 22. Erratum in: Bioinformatics. 2010 Oct 1;26(19):2499.

2.

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.

Harris EY, Ponts N, Le Roch KG, Lonardi S.

Bioinformatics. 2012 Jul 1;28(13):1795-6. doi: 10.1093/bioinformatics/bts264. Epub 2012 May 3.

3.

BS Seeker: precise mapping for bisulfite sequencing.

Chen PY, Cokus SJ, Pellegrini M.

BMC Bioinformatics. 2010 Apr 23;11:203. doi: 10.1186/1471-2105-11-203.

4.

BRAT-nova: fast and accurate mapping of bisulfite-treated reads.

Harris EY, Ounit R, Lonardi S.

Bioinformatics. 2016 Sep 1;32(17):2696-8. doi: 10.1093/bioinformatics/btw226. Epub 2016 Apr 23.

PMID:
27153660
5.

BSMAP: whole genome bisulfite sequence MAPping program.

Xi Y, Li W.

BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.

6.

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.

Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.

Genome Biol. 2012 Oct 3;13(10):R82. doi: 10.1186/gb-2012-13-10-r82.

7.

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Li B, Dewey CN.

BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323.

8.

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.

Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE.

BMC Bioinformatics. 2013 Nov 21;14:337. doi: 10.1186/1471-2105-14-337.

9.

GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

Manconi A, Orro A, Manca E, Armano G, Milanesi L.

PLoS One. 2014 May 19;9(5):e97277. doi: 10.1371/journal.pone.0097277. eCollection 2014.

10.

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.

Akman K, Haaf T, Gravina S, Vijg J, Tresch A.

Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.

11.

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.

12.

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.

PMID:
23603334
13.

MethylCoder: software pipeline for bisulfite-treated sequences.

Pedersen B, Hsieh TF, Ibarra C, Fischer RL.

Bioinformatics. 2011 Sep 1;27(17):2435-6. doi: 10.1093/bioinformatics/btr394. Epub 2011 Jun 30.

14.

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.

15.

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.

Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J.

Bioinformatics. 2015 Jun 15;31(12):2040-2. doi: 10.1093/bioinformatics/btv089. Epub 2015 Feb 13.

16.

Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis.

Rohde C, Zhang Y, Jurkowski TP, Stamerjohanns H, Reinhardt R, Jeltsch A.

Nucleic Acids Res. 2008 Mar;36(5):e34. doi: 10.1093/nar/gkn083. Epub 2008 Feb 22.

17.

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

Zhang J, Kobert K, Flouri T, Stamatakis A.

Bioinformatics. 2014 Mar 1;30(5):614-20. doi: 10.1093/bioinformatics/btt593. Epub 2013 Oct 18.

18.

A parallel and sensitive software tool for methylation analysis on multicore platforms.

Tárraga J, Pérez M, Orduña JM, Duato J, Medina I, Dopazo J.

Bioinformatics. 2015 Oct 1;31(19):3130-8. doi: 10.1093/bioinformatics/btv357. Epub 2015 Jun 10.

19.

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

Liao Y, Smyth GK, Shi W.

Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13.

PMID:
24227677
20.

Objective and comprehensive evaluation of bisulfite short read mapping tools.

Tran H, Porter J, Sun MA, Xie H, Zhang L.

Adv Bioinformatics. 2014;2014:472045. doi: 10.1155/2014/472045. Epub 2014 Apr 15.

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