Opentrons Protocol Library

The Opentrons Protocol Library is a central collection of automated biology workflows written for the Opentrons OT-2 using the OT-2 Python Protocol API (version 2). It exists to help labs automate common bench tasks, share reproducible procedures, and accelerate onboarding: protocols are provided as readable Python files or as parameterized templates, and many are marked as Featured or Opentrons Verified after in-house testing. The library complements the open-source Opentrons API and desktop app code on GitHub and is intended to be accessible to bench scientists with basic coding and wet-lab experience. Capabilities in the library cover a broad set of routine molecular biology tasks. You will find end-to-end NGS library-prep workflows (for example, Illumina Nextera XT and Swift 2S Turbo kits), magnetic-bead cleanups and size selection workflows (e.g., Omega Bio-tek Mag-Bind TotalPure NGS), PCR prep and master-mix assembly, normalization and cherrypicking routines, serial dilutions and plate transfers. Many protocols expose customization fields so you can pick sample counts, pipette types (P20/P50/P300 single- or multi-channel), tip types, bead ratios, elution volumes and module usage. Several verified protocols include links to application notes and recommended consumables and deck layouts, and some published workflows report practical throughput (for example, Swift 2S Turbo automation can prepare up to 16 libraries in under three hours when fully automated on the OT-2). Integration with the Opentrons ecosystem is a core strength. Protocols are built to run on OT-2 robots and to be executed from the Opentrons Run App (desktop Electron app). The Run App displays deck maps and protocol metadata (pipettes, modules, last update), guides calibration of labware, tipracks and pipettes, and runs the protocol on connected hardware. Protocols also declare compatible modules (Magnetic Module, Temperature Module, Thermocycler, Heater-Shaker) and labware; the library provides setup instructions for where to place reagents on the deck and which tips or module blocks to use. If you prefer a no-code approach, the library links to a graphical protocol creator so you can build and parameterize protocols without hand-editing Python. For code-savvy users, workflows can be downloaded as Python files for local editing and extension using the Opentrons API. Typical workflow to use a library protocol: find a Featured or Verified protocol that matches your assay, set the customization fields (sample count, pipette/tip choices, mount selection, reagent volumes), download the protocol file, upload it into the Opentrons Run App, set up your deck according to the provided deck map, calibrate labware and pipettes in the app, and run. For programmatic or advanced needs you can edit the downloaded Python protocol directly using the Opentrons API and test changes using emulation tools. The project is maintained on GitHub under an open license (contributors are welcome to file issues or submit pull requests), so labs and developers can contribute new protocols, report bugs, or adapt existing methods for their hardware and consumables.