Fig. 1

Graphical overview of the SCAPP algorithm. (A) The metagenomic assembly graph is created from the sample reads. (B) The assembly graph is annotated with read mappings, presence of plasmid specific genes, and node weights based on sequence length, coverage, and plasmid classifier score. (C) Potential plasmids are iteratively peeled from the assembly graph. An efficient algorithm finds cyclic paths in the annotated assembly graph that have low weight and high chance of being plasmids. Cycles with uniform coverage are peeled. (D) Confident plasmid predictions are retained using plasmid sequence classification and plasmid-specific genes to remove likely false positive potential plasmids