BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads

Bioinformatics

Volumn 28, Issue 13, 2012, Pages 1795-1796

  Harris, Elena Y ^a   Ponts, Nadia ^b,c   Le roch, Karine G ^b   Lonardi, Stefano ^a  

^a University of California Riverside   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; HYDROGEN SULFITE; SULFITE;

ARTICLE; COMPUTER PROGRAM; DNA METHYLATION; DNA SEQUENCE; GENOME; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY;

CYTOSINE; DNA METHYLATION; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EID: 84863995390     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts264     Document Type: Article

References (9)

1. Burrows, M. and Wheeler, D. (1994)Ablock sorting lossless data compression algorithm. Technical Report #124. Digital Equipment Corporation.
2. Chen, P.Y. et al. (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinform., 11, 203.
3. Cokus, S.J. et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219.
4. Ferragina, P. and Manzini, G. (2000) Opportunistic data structures with applications. In Proceedings of IEEE Foundation of Computer Science. pp.390-398. Redondo Beach, CA.
5. Frommer, M. et al. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. PNAS USA, 89, 1827-1831.
6. Harris, E.Y. et al. (2010) BRAT: bisulfite-treated reads analysis tool. Bioinformatics, 26, 572-573.
7. Krueger, F. and Andrews, S. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
8. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
9. Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.