ArticleMicrobiome2021
SCAPP: an algorithm for improved plasmid assembly in metagenomes.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
47 citing papers in PubMed, 71 citations in OpenAlex.
- CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.Gut microbes · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.Microbiome · 2026Article
- ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.Microbiome · 2025Article
- Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.Briefings in bioinformatics · 2025Article
- Node role of wild boars in virus circulation among wildlife and domestic animals.Nature communications · 2025Article
- Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.NAR genomics and bioinformatics · 2025Article
- Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment.Genome biology · 2025Article
- Unveiling plasmid diversity and functionality in pristine groundwater.Environmental microbiome · 2025Article
- Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.The ISME journal · 2025Article
- Article
- Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.Frontiers in microbiology · 2025Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.ACS synthetic biology · 2024Article
- Chromosomal Type II Toxin-Antitoxin Systems May Enhance Bacterial Fitness of a Hybrid PathogenicToxins · 2024Article
- Review
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.bioRxiv : the preprint server for biology · 2024Article
- PlasCAT: Plasmid Cloud Assembly Tool.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundMetagenomic 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.
resultsWe 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.
conclusionsSCAPP 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 . Video abstract.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.