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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.


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.


BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.

Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M.

BMC Genomics. 2013 Nov 10;14:774. doi: 10.1186/1471-2164-14-774.


Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.

Prezza N, Vezzi F, Käller M, Policriti A.

BMC Bioinformatics. 2016 Mar 2;17 Suppl 4:69. doi: 10.1186/s12859-016-0910-3.


The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing.

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE.

Bioinformatics. 2010 Jan 1;26(1):38-45. doi: 10.1093/bioinformatics/btp614. Epub 2009 Oct 27.


MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.

Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY.

BMC Genomics. 2015;16 Suppl 12:S11. doi: 10.1186/1471-2164-16-S12-S11. Epub 2015 Dec 9.


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.


Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA.

Nucleic Acids Res. 2014 Apr;42(6):e43. doi: 10.1093/nar/gkt1325. Epub 2014 Jan 3.


BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data.

Hu K, Ting AH, Li J.

BMC Bioinformatics. 2015 Jul 11;16:220. doi: 10.1186/s12859-015-0649-2.


BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data.

Liang F, Hao L, Wang J, Shi S, Xiao J, Li R.

Comput Biol Chem. 2016 Dec;65:173-177. doi: 10.1016/j.compbiolchem.2016.09.003. Epub 2016 Sep 9.


Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.

Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, von Haeseler A.

PLoS One. 2012;7(7):e41528. doi: 10.1371/journal.pone.0041528. Epub 2012 Jul 20.


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.


Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS).

Yang Y, Sebra R, Pullman BS, Qiao W, Peter I, Desnick RJ, Geyer CR, DeCoteau JF, Scott SA.

BMC Genomics. 2015 May 6;16:350. doi: 10.1186/s12864-015-1572-7.


Fast and sensitive mapping of bisulfite-treated sequencing data.

Otto C, Stadler PF, Hoffmann S.

Bioinformatics. 2012 Jul 1;28(13):1698-704. doi: 10.1093/bioinformatics/bts254. Epub 2012 May 10.


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.


An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.

Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH.

Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291. Epub 2010 Jun 18.


GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data.

Benoukraf T, Wongphayak S, Hadi LH, Wu M, Soong R.

Nucleic Acids Res. 2013 Feb 1;41(4):e55. doi: 10.1093/nar/gks1281. Epub 2012 Dec 24.


Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.

Stevens M, Cheng JB, Li D, Xie M, Hong C, Maire CL, Ligon KL, Hirst M, Marra MA, Costello JF, Wang T.

Genome Res. 2013 Sep;23(9):1541-53. doi: 10.1101/gr.152231.112. Epub 2013 Jun 26.


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.


AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing.

Chen J, Lutsik P, Akulenko R, Walter J, Helms V.

J Bioinform Comput Biol. 2014 Dec;12(6):1442005. doi: 10.1142/S0219720014420050.


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