SCAPP: An algorithm for improved plasmid assembly in metagenomes

Abstract

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 meta-plasmidSPAdes across this wide range of datasets. Availability: https://github.com/Shamir-Lab/SCAPP

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

“…Within public-health metagenomic research it is vital we utilise MAGs in conjunction with other methods (e.g. targeted AMR [66], long-read sequencing, plasmid specialised assembly approaches [48], and read-based sequence homology search [11]) before drawing biological or epidemiological conclusions.…”

“…read-based methods) in public health metagenomic research when short-read sequencing is used. For example, targeted AMR [68], plasmid specialised assembly approaches [65], and read-based sequence homology search [11]. Without this, MAG-based methods are insu cient to thoroughly pro le the resistome and provide vital epidemiological data for metagenomic data.…”

“…The particularly poor plasmid binning performance is likely attributable to the known di culties in assembly of plasmids from short-read data [47]. Therefore, binning e ciency might improve with use of long-read sequencing or assembly methods optimised for recovering plasmids [47] (such as SCAPP [48]). Despite its lower e ective sequencing depth and higher error rates, incorporating long-read sequencing has been shown to improve overall MAG binning [49] and facilitate metagenomic characterisation of plasmids [50].…”

“…This di erence might be attributed to the known di culties in assembly of plasmids from short-read data [64]. Therefore, binning e ciency might improve if we use DNA sequencing and assembly methods optimised for recovering plasmids [45] (such as SCAPP [65]).…”

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

“…Many bioinformatic tools have been recently developed to overcome this challenge in short-read sequencing. Examples of them are PlasmidFinder, cBar, PLACNET, (meta)plasmidSPAdes, recycler, plasflow, MOB-suite, mlplasmids, plaScope, gplas, plasClass, plasGUN,SCAPP, metaviralSPAdes ( Zhou and Xu, 2010 ; Carattoli et al., 2014 ; Rozov et al., 2017 ; Vielva et al., 2017 ; Arredondo-Alonso et al., 2018 ; Arredondo-Alonso et al., 2020 ; Krawczyk et al., 2018 ; Robertson and Nash, 2018 ; Royer et al., 2018 ; Antipov et al., 2019 , 2020 ; Fang et al., 2020 ; Pellow et al., 2020a , Pellow et al., 2020b ; Pellow et al., 2020 , 2020 ). These tools identify plasmids and viruses in metagenomic samples or bacterial isolates in a variety of ways, ranging from the simpler approach of blasting against a plasmid database (PlasmidFinder, MOB-suite) to the use of more complex deep neural networks (cBar, PlasFlow).…”