SCAPP

SCAPP assembles plasmid sequences from metagenomic assembly graphs to recover full plasmids from complex microbial communities.

Key Features:

• Algorithmic Innovation: Builds upon the Recycler algorithm and incorporates plasmid-specific biological insights to improve plasmid assembly accuracy.
• Performance Superiority: Demonstrated improved performance in benchmarks on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset compared to Recycler and metaplasmidSPAdes.
• Novel Assessment Procedure: Employed parallel sequencing data from cow rumen samples to generate plasmidome and metagenome datasets for a novel evaluation approach validating plasmid recovery.

Scientific Applications:

• Microbial ecology: Recovery of complete plasmids from metagenomes to study plasmid diversity and distribution within microbial communities.
• Antibiotic resistance surveillance: Identification and assembly of plasmids that carry antibiotic resistance genes from complex samples.
• Pathogen evolution studies: Reconstruction of plasmids involved in horizontal gene transfer to investigate evolutionary dynamics among bacteria.
• Clinical plasmid characterization: Assembly of clinically relevant plasmids from human gut plasmidome and microbiome datasets to inform studies of host-associated plasmids.

Methodology:

Uses an assembly graph approach tailored to plasmid DNA, builds on the Recycler algorithm, and integrates biological knowledge about plasmids to distinguish plasmid sequences from chromosomal DNA.