SCAPP: An algorithm for improved plasmid assembly in metagenomes

Motivation: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids, which are less studied or understood. In order to assist in the study of these plasmids we developed SCAPP (Sequence Contents Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. Results: SCAPP builds on some key ideas from the Recycler plasmid assembly algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome that we generated. We also created a parallel plasmidome-metagenome cow rumen sample and used it to create a novel assessment procedure. In most cases SCAPP performed better than or similar to Recycler and metaplasmidSPAdes across this wide range of datasets. Availability: https://github.com/Shamir-Lab/SCAPP