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Workflow and implementation of PropagAtE. (A) Workflow of PropagAtE, including data input, read alignment processing, and results output. Example of read coverage profiles for two active Bacillus licheniformis DSM13 prophages with all reads (B) or 5% subsampled reads (C) aligned, respective to the conceptual diagram in Fig. 1D. For panels B and C, statistics for coverage, Cohen’s d effect size, and prophage/host coverage ratio are shown.
