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Long-Read Plasmid Sequencing and Assembly Using Nanopore Sequencing-Based Workflows
Published on: July 7, 2026
plsMD: a plasmid reconstruction tool from short-read assemblies
Maryam Lotfi1, Deena Jalal2, Ahmed A Sayed3,4
1Department of Basic Research, Genomics and Metagenomics Program, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
BMC Bioinformatics
|August 14, 2026
Summary
We developed plsMD, a new tool for reconstructing complete plasmid sequences from short-read sequencing data. This advancement aids in tracking antimicrobial resistance genes and understanding plasmid evolution.
Area of Science:
- Genomics
- Microbiology
- Bioinformatics
Background:
- Whole genome sequencing is crucial for antimicrobial resistance surveillance.
- Reconstructing plasmid sequences from short-read data is challenging due to repetitive sequences and assembly fragmentation.
- Existing tools have limitations in full plasmid reconstruction, hindering downstream analyses.
Purpose of the Study:
- To present plsMD, a novel computational tool for accurate full plasmid reconstruction from short-read assemblies.
- To enable robust plasmid analysis for studying antimicrobial resistance spread and evolution.
Main Methods:
- plsMD integrates Unicycler assemblies with replicon and plasmid sequence databases.
- It employs contig manipulation to guide plasmid reconstruction.
- The tool was evaluated on a benchmark dataset and a novel dataset of bacterial isolates.
Main Results:
- plsMD outperformed existing tools in plasmid reconstruction accuracy.
- Achieved high recall, precision, and F1 scores on both benchmark (91.3%, 95.5%, 92.0%) and novel (77.6%, 88.9%, 74.5%) datasets.
- Supports single-sample analysis (reconstruction, annotation) and batch-sample analysis (phylogenetics).
Conclusions:
- plsMD offers a robust solution for full plasmid reconstruction from short-read sequencing data.
- It significantly advances plasmid analysis for studying antimicrobial resistance.
- Facilitates research into plasmid-mediated antimicrobial resistance spread and evolution.
