Whether you are working with SARS-CoV-2, HIV-1, or any other viral pathogen, sequence analysis has become an important tool in many aspects of virology and immunology: from understanding viral evolution, transmission, and emergence of drug and/or antibody resistance, to designing novel vaccine immunogens and clinical interventions.
This workshop will provide a step-by-step guideline on how to use sequence visualization and analysis tools available from the LANL database (hiv.lanl.gov) to build a pipeline from sequence reads to phylogenetic trees. Highlights include: creating a sequence alignment, visualizing sequence diversity, setting up a genetic signature analysis, and searching the LANL sequence and antibody databases.
Examples and hands-on exercises will be provided. While most will be using HIV env sequences, the analysis pipeline and tools can be applied to any pathogen. For HCV and SARS-CoV-2 tailored versions of the tools are available.
This workshop will be held in room 47-215 of the Carmichael Bldg and will be IN-PERSON ONLY.
Registration will be limited to the first 30 registrants.
Participants are required to bring their own laptops with Wi-Fi access for hands-on practice with each of the tools presented during the workshop. Additionally, we request users to download and install the free sequence editing software AliView.
Testing and masking requirements will be observed as described in Duke’s current guidelines as they stand on the day of the workshop.