PASS-bis: A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads

Bioinformatics

Volumn 29, Issue 2, 2013, Pages 268-270

  Campagna, Davide ^a   Telatin, Andrea ^a   Forcato, Claudio ^a   Vitulo, Nicola ^a   Valle, Giorgio ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN SULFITE; SULFITE;

ALGORITHM; ARTICLE; COLOR; DNA METHYLATION; DNA SEQUENCE; GENOMICS; HUMAN; METHODOLOGY; SEQUENCE ALIGNMENT;

ALGORITHMS; COLOR; DNA METHYLATION; GENOMICS; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SULFITES;

MLCS; MLOWN;

EID: 84872573541     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts675     Document Type: Article

References (9)

1. Campagna, D. et al. (2009) PASS: a program to align short sequences. Bioinformatics, 25, 967-968.
2. Chen, P.Y.T. et al. (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203.
3. Cokus, S.J. et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219. (Pubitemid 351380251)
4. Grunau, C. et al. (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acid Res., 29, e65.
5. Kreck, B. et al. (2012) B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. Bioinformatics, 28, 428-429.
6. Krueger, F. and Andrews, S. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
7. Massingham, T. and Goldman, N. (2012) Error-correcting properties of the SOLiD Exact Call Chemistry. BMC Bioinformatics, 13, 145.
8. Ondov, B.D. et al. (2010) An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System. Bioinformatics, 26, 1901-1902.
9. Xi, Y. and Li, W. (2009) BSMAP: whole genome bisulfite sequence mapping program. BMC Bioinformatics, 10, 232.