 kineticsTools [![Circle CI](https://circleci.com/gh/PacificBiosciences/kineticsTools.svg?style=svg)](https://circleci.com/gh/PacificBiosciences/kineticsTools)
 
Note this repo only includes models for RSII chemistries, recent Sequel / Sequel II data should be analyzed with a recent version of SMRT Analysis https://www.pacb.com/support/software-downloads/

Tools for detecting DNA modifications from single molecule, real-time (SMRT&reg;) sequencing data. This tool implements the P_ModificationDetection module in SMRT&reg; Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol. Researchers interested in understanding or extending the modification detection algorthims can use these tools as a starting point. 

Academic Publications:
 * [Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing](http://nar.oxfordjournals.org/content/40/4/e29)
 * [The methylomes of six bacteria](http://nar.oxfordjournals.org/content/early/2012/10/02/nar.gks891.full)

Documentation:
 * [Tool documentation](http://github.com/PacificBiosciences/kineticsTools/blob/master/doc/manual.rst)
 * [Methods description](http://github.com/PacificBiosciences/kineticsTools/blob/master/doc/whitepaper/kinetics.pdf)

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