The Production Bioinformatics team is in charge of the day to day production of polished, high quality sequence data, and acts as a liaison between the sequencing laboratory and other bioinformatics teams.
Responsibilities start with working with lab technicians, sequencer manufacturers and system administrators to maintain a stable informatics environment for the raw data generated by the sequencing machines. Upon completion, each sequencing run is passed through a quality evaluation based on basecalling confidence and alignment to a reference genome. We specifically look for consistency in the basecalling across the entire read, and a high percentage of reads aligning to the given reference with a low error rate. Approved runs are then passed on to collaborators or bioinformaticians at the CNAG in a standardised format. Runs with quality issues undergo trouble shooting with the help of the CNAG Sequencing Group and manufacturers.
In addition, the team is responsible for developing an in-house Lab Information Management System (LIMS) to track the status of samples from a wide variety of projects as they progress through reception, preparation, sequencing and analysis. This system stores project, sample and run information along with analysis results, which are scanned by our in-house software scan for potential problems.
When combined, these various aspects of the Production Bioinformatics team maintain the steady production of high quality data at the CNAG.