RT Journal Article
SR Electronic
T1 SCAPP: An algorithm for improved plasmid assembly in metagenomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.12.903252
DO 10.1101/2020.01.12.903252
A1 David Pellow
A1 Alvah Zorea
A1 Maraike Probst
A1 Ori Furman
A1 Arik Segal
A1 Itzhak Mizrahi
A1 Ron Shamir
YR 2020
UL http://biorxiv.org/content/early/2020/08/12/2020.01.12.903252.abstract
AB 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 bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples.Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids.We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets.Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases, and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.Competing Interest StatementThe authors have declared no competing interest.