Useful links

1. SAAP-RRBS - a comprehensive software that integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting, and visualization..
2. methylKit - an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.
3. BSmooth - an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates.
4. BiQ Analyzer HT - achieving the alignment, quality filtering and data representation, perfects BiQ Analyzer from high-throughput bisulfite sequencing.
5. QDMR - a platform-free and species-free software is built to be a quantitative approach to quantify methylation difference.
6. Bis-SNP - a bisulfite SNP caller based on Genome Analyzer Toolkit(GATK) map-reduce framework, can simultaneously get better SNPs and accurate methylation levels.
7. Bismark - an enhanced version of Bowtie to align bisulfite-treated reads, is a next-generation sequencing analysis software, which simultaneously contain a methylation information extractor to extract methylation statu of different types of cytosine.
8. BRAT-bw - implements Burrows-Wheeler transform algorithm to align bisulfite sequencing reads of single or paired-end to a reference genome. The end-trim tool and remove-dupl make it more easy for preparation, and the conversion tool produces SAM file for convenient subsequent analysis.
9. BS Seeker - a python script based software used for BS reads mapping. It implements Bowtie to do the alignment and also provides conversion tool to convert alignment to SAM/BAM file for subsequent analysis.
10. BSSim - a bisulfite sequencing simulator based on the Python language and a cross-platform BS-seq simulator, whose output read datasets suit for most of the next-generation sequencing platforms.
11. B-SOLANA - based on SOLiD sequencing platform, is designed for bisulfite sequencing mapping and methylation level determination of different cytosine contexts.
12. BSMAP - a bisulfite-treated short reads mapping software based on SOAP, combines hashing and bitwise masking algorithm to perform fast and accurate bisulfite mapping.
13. ERNE - short for extended randomized numerical aligner, is a mapping software targeting accurate alignment of NGS reads and bisulfite-treated reads as well.
14. GBSA - Genome Bisulfite Sequencing Analyser (GBSA) is an academical and open-source software (GPL) capable of analyzing whole-genome bisulfite sequencing data.
15. KARMA - an index and K-tuple based mapping software, can map shotgun sequencer FASTQ reads to a reference genome.
16. Methyl-Analyzer - designed for subsequently analyzing alignment data produced by Methyl-MAPS, supports parsing mate-pair reads, filtering methylated/unmethylated fragments, estimating CpG methylation probability and visualization of DNA methylation profiles.
17. MethMarker - an epigenetic primer-design and biomarker-optimize software.
18. Methyl Coder - Program that generates per-base methylation data given a set of bisulfite-treated reads. It provides the option to use either of two existing short-read aligners, each with different strengths. It accounts for soft-masked alignments and overlapping paired-end reads.
19. MethylDraw - a simple visualization tool, based on perl language, to display the DNA methylation level using bisulfite sequencing data. It can produce the images with the methylation level of CpG sites for several samples treated in different conditions.
20. Meth Tools 2.0 - a web tool for the second generation and analysis of DNA methylation patterns from bisulfite sequencing raw data. It can compare the sequence data of the PCR products with the genomic sequence, generate graphical representations of methylation information and perform other numerical analysis.
21. NGSmethDB - a database of DNA methylation at single-base resolution, stores methylation datasets of different tissues, and are available for data mining and visualization with a browser.
22. PASH - a multipurpose software, designed for alignment and integrative analysis of genomic and epigenetic variation through massively parallel DNA sequencing, takes advantage of gapped k-mer alignment and can run on diverse hardware platforms.
23. RMAP - a NGS short-read mapping software. The update version with several modifications such as lower memory consumption, paired-end reads mapping, collection of ambiguously mapping reads and bisulfite-treated reads mapping.
24. RRBSMAP - designed for reduced representation bisulfite sequencing(RRBS), is a short-read mapping software without any need of preprocessing or postprocessing. RRBSMAP, as a extension of BSMAP, only index the enzyme digestion sites, making the RRBSMAP great reduction of memory consumption.
25. BS Seeker - a python script based software used for BS reads mapping. It implements Bowtie to do the alignment and also provides conversion tool to convert alignment to SAM/BAM file for subsequent analysis.
26. EpiExplorer - A web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing.