Constructing a quality control platform for plasmid verification

Plasmids are ubiquitous tools found in molecular biology laboratories around the world, where they serve a variety of uses such as transferring DNA sequences into a target cell, modifying gene expression, or monitoring biological pathways and components. Addgene was founded as a nonprofit repository for DNA-based biological reagents, such as plasmids, in order to accelerate scientific research by improving access to high-quality research materials. Our quality control process has evolved over time to keep pace with DNA sequencing technologies where we now fully sequence every plasmid deposited with us. In order for our quality control team to analyze more than 1000 sequences each month, we needed to automate our existing bioinformatics scripts and centralize a standardized workflow. Using Nextflow, we created a workflow for processing an entire sequencing run from an Illumina MiSeq instrument. The raw sequencing data is retrieved, converted to FASTQ, cleaned with various programs from the BBTools suite, and assembled into complete, circularized sequences using open-source sequence assembly tools such as SPAdes and Shovill. We deployed our workflow in Seqera Platform so that anyone on our quality control team could launch the workflow, without needing to use a command line interface. Additionally, we reduced our compute costs by provisioning the required resources as needed, while allowing for easy scaling should our intake or turn-around time requirements change. With the success of our first workflow in Seqera Platform, we are looking to add new modules to further automate sequence analysis by screening for contaminant sequences in the FASTQ sequence reads and provide a quality assessment of the final assembled sequence.