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

Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing

(2013) Junwen Wang et al.   BMC GENOMICS

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

(2012) Elena Y. Harris et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

(2011) Yuanxin Xi et al.   BIOINFORMATICS

MethylCoder: software pipeline for bisulfite-treated sequences

(2011) B. Pedersen et al.   BIOINFORMATICS

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE