SeqMonitor: influenza analysis pipeline and visualization

Unprecedented sequencing effort has led to daily submissions of influenza genomes to public repositories such as the NCBI GenBank. With the decreasing cost of genome sequencing, it is expected that rapidly evolving viruses such as influenza will be sampled in even greater depth in the future. Keeping analyses up to date and managing this data is a prime concern for researchers and public-health officials alike. We have developed an influenza sequence pipeline, polymorphism data warehouse, and an interactive web-based analysis program to assist in managing the flow of sequence data. The system provides a framework for studying polymorphic associations with various metadata, for downloading subsets based on metadata criteria, as well as for tracking polymorphisms geographically and temporally. SeqMonitor is accessible at http://ratite.cs.dal.ca/SeqMonitor.