Related Experiment Video
Updated: Dec 15, 2025
12:08
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
5.6K
Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process
Rei Kajitani1, Dai Yoshimura1, Yoshitoshi Ogura2,3
1School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
Summary
Platanus_B is a new de novo assembler that accurately assembles bacterial genomes using short DNA reads. It improves hybrid assembly with long reads and achieves high accuracy for genomic surveillance and phylogenomic analyses.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- De novo assembly of short DNA reads is crucial for large-scale projects and epidemiological variant analyses.
- Existing tools often lack the accuracy needed for comparing closely related bacterial strains.
Purpose of the Study:
- To develop a de novo assembler, Platanus_B, with enhanced accuracy for bacterial genome assembly.
- To improve hybrid assembly strategies combining short and long DNA reads.
Main Methods:
- Platanus_B employs iterative error-removal algorithms for de novo assembly.
- Evaluated Platanus_B's performance on bacterial genomes using benchmarks.
- Assessed hybrid assembly strategies with short (Illumina) and long (Nanopore) reads.
Main Results:
- Platanus_B demonstrated superior accuracy and contiguity compared to existing tools.
- Hybrid assembly with Platanus_B achieved near full-length bacterial genomes.
- Short-read-only assemblies with Platanus_B yielded ≥90% exact coding sequences.
- Incorporating short reads improved the fine-scale accuracy of long-read-only assemblies.
Conclusions:
- Platanus_B is a highly accurate de novo assembler for bacterial genomes.
- It effectively enhances hybrid assembly strategies for improved genome completeness and accuracy.
- Platanus_B is suitable for comprehensive genomic surveillance and high-resolution phylogenomic studies of bacteria.
