78 StaPH-B: state public health bioinformatics

Dr. Erin Young and Dr Kelsey Florek join us to talk about StaPH-B, a US state public health bioinformatics group. They also give some insights into the popular SARS-CoV-2 pipeline cecret. Website: staphb.org/ Cecret Pipeline: github.com/CDCgov/SC2CLIA Kelsey explains that StaPH-B was created to facilitate collaborations between bioinformaticians in state public health laboratories, especially those just getting started with sequencing and understanding the data generated. The organization provides a conduit of communication and expertise among different laboratories, feeding into projects funded by the NIH, CDC, and other grant agencies. Erin highlights StaPH-B's diverse membership with different levels of expertise, which provides excellent learning opportunities. The organization uses a Slack workspace, with almost 400 members and over 50 channels dedicated to different activities related to bioinformatics, providing a valuable resource for bioinformaticians to seek out answers to questions and ideas. The hosts ask Kelsey about who can join StaPH-B, and Kelsey clarifies that while it was initially founded for state public health bioinformaticians, it's open to everyone, and the content is focused on state public health activities. They discuss some of the achievements of StaPH-B, with Kelsey hailing the Slack workspace, collaborations on GitHub, Docker, and collaborative workflows as hugely successful. Additionally, Erin thinks that StaPH-B's training activities, including the Staph-B Toolkit, training sessions, and videos, ensure that knowledge and expertise are shared. The conversation moves towards the Cecret pipeline, one of Erin's bioinformatics pipelines for SARS-CoV-2. She explains that the pipeline was developed during the pandemic, with the idea of using the Arctic group's protocol for sequencing SARS-CoV-2 on the Nanopore sequencing platform. However, Erin needed a bioinformatic pipeline that was Illumina-based, as it would have been easier to sequence SARS-CoV-2 on the MiSeq, rather than the Nanopore sequencing platform. Cecret pipeline was developed using BWA as the default aligner and is for viral-based sequencing with a known, reliable reference. Erin points to the SEQret pipeline tutorials and the monthly videos produced by StaPH-B that outline various state laboratory projects as tips for people entering the field. Lastly, Kelsey emphasizes the importance of finding a use case to start building a centralized source of expertise in bioinformatics and making knowledge accessible by having a common resource that's easy to access. In a previous episode, the guest speakers discussed the evolution of COVID genome analysis workflows and how they have changed over time due to the increasing amount of data being analyzed. They mentioned the use of different workflows such as Secret, NF Core, Monro, and Next Flow Optic Pipeline, each with their own unique features and popularity. Erin, the creator of Secret, talked about how paranoid she was when sharing her workflow publicly and how she would track every fork of her repository to ensure that the changes made to her code were scientifically sound. The workflow has undergone gradual changes and fewer bugs since its creation, with no dramatic turning point. Its name, “Secret,” was inspired by a hiking landmark in Northern Utah that Erin found meaningful. The speakers emphasized the importance of managing and working with the increasing amounts of COVID data being analyzed, as well as connecting it to public health. In conclusion, StaPH-B and workflows such as Secret are playing a significant role in the field of bioinformatics and COVID genome analysis. Collaborations and resources like StaPH-B are essential in sharing knowledge and expertise among different laboratories, allowing for the successful completion of projects funded by the NIH, CDC, and other grant agencies.