Mapping target bisulfite sequencing reads to a reference

Question

[tomasz.jurkowski]

Hi,

I'm looking for software to map the sequencing reads from bisulfite treated synthetic DNA to a reference sequence. What I'm interested to get is the alignment to the reference, since I need to process the data further to extract preferred methylation sites.Do you know any software that would be suitable for this?

Thanks a lot in advance,
Tomek

Answer 1

[Antonio R. Franco]

ttp://lmgtfy.com/?q=mapping+genome+bisulphyte

segemehl if working with CpG

Bismark if working with CpG and non canonical methylations as in plant CHH CHG

BSMAP

Some more are available, but these are popular

Answer 2

[dora]

http://www.bioinformatics.babraham.ac.uk/projects/bismark/

Answer 3

[jomo018]

QuasR library in R. The alignment portion in both QuasR and Bismark is actually performed by Bowtie.