Platanus_B

Platanus_B assembles bacterial genomes de novo to produce accurate, contiguous assemblies for high-resolution phylogenomic and epidemiological analyses.

Key Features:

• Iterative Error-Removal Algorithms: Employs multiple iterations of error-removal to refine assemblies and improve contiguity and accuracy for distinguishing closely related strains.
• Hybrid Assembly Capabilities: Integrates Illumina paired-end short reads with Oxford-Nanopore or PacBio long reads to generate near full-length assemblies with enhanced accuracy.
• Short-Read Efficiency: Can produce high-quality assemblies using only short reads that capture ≥90% of exact coding sequences in most bacterial genomes.
• Long-Read Accuracy Enhancement: Uses short-read data to improve the fine-scale accuracy of long-read assemblies for detailed phylogenomic analyses.
• Utility Functions: Provides a "combine" command to merge multiple assemblies.

Scientific Applications:

• Genomic Surveillance: Produces accurate, contiguous assemblies for surveillance of bacterial pathogens.
• High-Resolution Phylogenomics: Supports phylogenomic analyses that require fine-scale variant resolution across strains.
• Epidemiological Investigations: Facilitates outbreak and transmission studies by distinguishing closely related bacterial strains.

Methodology:

Performs iterative sequence extensions, gap closures, and error removals and accommodates Illumina paired-end, Oxford-Nanopore, and PacBio reads.