Dryad v4.0.0 is now compatible with Nextflow DSL 2 and features enhanced efficiency and usability through a major restructuring. The resulting workflow is divided into two distinct branches to address different types of investigation needs.
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High-Resolution Analysis: For a detailed examination of an individual outbreak, an alignment-based approach can be utilized. This fine tune analysis incorporates tools such as snp-dists, iq-tree2, and parsnp to infer a phylogenetic tree.
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Low-Resolution Historical Analysis: For a broader historical insight across multiple outbreaks, an alignment-free approach can be employed. This approach uses mashtree to infer a phylogenetic tree based on mash distances.