ArticleBioinformatics and biology insights2026
PCNE: A Tool for Plasmid Copy Number Estimation.
Article in Bioinformatics and biology insights, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The identification of plasmids from assembled genomes is well supported by numerous different tools, yet very few incorporate a plasmid copy number estimation step. This limits a comprehensive plasmid analysis, often leaving researchers to perform copy number estimation independently, leading to a lack of standardization. Plasmid Copy Number Estimator (PCNE) addresses this by providing an accessible and versatile command-line tool for estimating plasmid copy numbers directly from short-read sequencing data. Starting from standard input data like raw reads and a genome assembly, PCNE allows to apply a flexible normalization strategy, including an optional GC-bias correction, and is designed to complement existing plasmid detection pipelines. By simplifying and standardizing copy number estimation, PCNE, through the integration of state-of-art methodologies, aims to empower researchers to gain deeper insights into plasmid biology, particularly in studies of antimicrobial resistance and horizontal gene transfer.
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