Primer Design Pipeline

Description

• This pipeline is designed to design primers for a given genome and set of region of interests (ROIs) for Multiplex PCR reactions. It uses a tiled approach to design primers for a given set of ROIs. Each region is split into overlapping amplicons. Primers are designed for each amplicon and then filtered against the target genome and other species. The remaining primers are then optimized using the SADDLE algorithm.

Requirements

Config files

• Please use the config.yaml file and primer3_settings.yaml to adjust the settings of the pipeline
• For a detailed overview of how to run the pipeline please refer to this file

Software

• This file contains a list of all required software to run the pipeline. This pipeline uses the mamba environment manager to install all required software. If run using snakemake, the --use-conda flag will automatically install all required software using the environment.yaml file.

• This file provides a detailed overview of the steps employed in the pipeline and how each of its modules/steps work. It is very detailed.