- pbcommand PacBio core data models, interface to the PacBio Tool Contract for defining pipeline tasks, and web services client to SMRT Link.
- pbsmrtpipe PacBio workflow Engine. Supports file chunking and submission to schedulers, such as SGE and PBS.
- CramUnit Test unit library to call cram and generate jUnit XML for consumption by continuous integration systems, such as jenkins or bamboo.
- pbcommandR R interface to the common models and PacBio Tool Contract Interface
- pbreports PacBio library for computing metrics and generating Reports used in SMRT Analysis 2.x and SMRT Link.
- pbcoretools PacBio library for commandline tools to interface to PacBio DataSets and standard bioinformatic file formats (e.g., Fasta, Fastq)
- pymatgen Computation material science library used to interface to crystal structures and molecules for electronic structure calculations. Core library used the Materials Project.
- PacBio :: pysiv (python) Primary author: Internal Core pipeline testing framework used in SMRT Analysis 2.x. (Replaced by pbsmrtpipe.testkit)
- PacBio :: pysiv2 (python) Primary author, shared with @natecols: Extension of pbsmrtpipe with custom validation leveraging testkit
- PacBio :: smrtflow (Scala) Primary author, shared with @natecols @smcclellan7 and @skinner.
- PacBio :: Primary Analysis Engine (Scala) Maintainer: Internal Primary Analysis orchestration engine (akka + ZMQ) and Web services
- PacBio :: Data Transfer Services (Scala) Internal Primary author: data transfer services used in Primary Analysis
- MaterialsProject :: rockets (python) Primary author: Original Workflow engine using by the Materials Project. Was replaced by fireworks