| Resources |
Purpose |
URL |
Ref |
| RRBSMAP |
A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing |
http://rrbsmap.computational-epigenetics.org/ |
[92] |
| BSMAP |
Ahole genome bisulfite sequence mapping |
http://code.google.com/p/bsmap/ |
[48] |
| BS Seeker |
Precise mapping for bisulfite sequencing |
http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html |
[46] |
| Bismark |
Map and determine the Methylation state of BS-Seq read |
http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/ |
[47] |
| SOCS-B |
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System |
http://solidsoftwaretools.com/gf/project/socs/ |
[93] |
| BRAT |
Bisulfite-treated reads analysis tool |
http://compbio.cs.ucr.edu/brat/ |
[94] |
| BISMA |
Analysis of bisulfite Sequencing data from both unique and repetitive sequences |
http://biochem.jacobs-university.de/BDPC/BISMA/ |
[95] |
| BiQAnalyzerHT |
Locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing |
http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/ |
[49] |
| CpGviewer |
Sequence analysis and editing for bisulphite genomic sequencing projects |
http://xserve1.leeds.ac.uk/~iancarr/cpgviewer |
[50] |
| CpG PatternFinder |
Windows-based program for bisulphite DNA |
- |
[52] |
| CyMATE |
Bisulphite-based analysis of plant genomic DNA |
http://www.gmi.oeaw.ac.at/CyMATE |
[51] |
| GenomeStudio Software |
Analyzing data generated from Illumina assays |
- |
- |
| MethMarker |
Design, optimize and validate DNA methylation biomarkers for a given DMR |
http://methmarker.mpi-inf.mpg.de/ |
[96] |
| BDPC |
Bisulfite sequencing Data methylation analysis. |
http://biochem.jacobs-university.de/BDPC |
[97] |
| MethylCoder |
Software pipeline for bisulte-treated sequences |
https://github.com/brentp/methylcode |
[98] |
| QUMA |
Quantification tool for methylation analysis |
http://quma.cdb.riken.jp/ |
[53] |
CyMATE ,Cytosine Methylation Analysis Tool for Everyone; BSMAP, Bisulphite Sequence
Mapping Program, BISMA, Bisulfite Sequencing DNA Methylation Analysis;
BRAT,bisulte-treated reads analysis tool; DMR, differentially methylated DNA
region; QUMA, Quantification Tool For Methylation Analysis.