Base Modification Datasets and Software - PacificBiosciences/DevNet GitHub Wiki
A growing number of datasets and software tools showcase the capability of SMRT® Sequencing to detect DNA base modifications, including methylation.
For more base modification content, see the PacBio basemod application page.
See also the full Datasets, [Examples](How To's and Examples) and [Compatible Software](Compatible Software) pages.
Datasets
- [The Methylomes of Six Bacteria](The Methylomes of Six Bacteria)
- [Statistical Modeling of Enzyme Kinetics for Base Modification Detection](CRF for Base Modification)
- [E. coli K12 MG1655 Methylome](E coli K12 MG1655 Methylome)
Examples and How-To's
- [Detect base modifications with SMRT Sequencing](Detect Base Modifications with SMRT Sequencing)
Software Tools
- kineticsTools: Python code for kinetic analysis
- R-kinetics: R package for kinetic analysis
- MotifMaker: bundled in SMRT Analysis since v1.3.3
- motif-finding: R code for motif analysis