SCAPP: an algorithm for improved plasmid assembly in metagenomes

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across species confer antibiotic resistance. plasmids are generally less studied understood than their hosts. Part reason for this is insufficient computational tools enabling analysis in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm tool assemble plasmid sequences from sequencing. builds on some key ideas Recycler while improving assemblies by integrating biological knowledge about plasmids. compared performance metaplasmidSPAdes simulated metagenomes, real human gut microbiome samples, a plasmidome dataset we generated. also created metagenome data same cow rumen sample used parallel create novel assessment procedure. Overall, outperformed wide range datasets. Conclusions an easy use Python package enables full It existing assemblers most cases assembled clinically relevant samples generated such as plasmidome. open-source software available from: https://github.com/Shamir-Lab/SCAPP .