Base Modification Datasets and Software

A growing number of datasets and software tools showcase the capability of SMRT® Sequencing to detect DNA base modifications, including methylation. Are we missing any? Please email devnet at pacificbiosciences dot com so we can update the list.

For more base modification content, see the PacBio basemod application page.

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

• R-kinetics: R package for kinetic analysis
• MotifMaker: bundled in SMRT Analysis since v1.3.3
• motif-finding: R code for motif analysis
• kineticsTools: Python code for kinetic analysis