HyAsP

HyAsP identifies, bins, and assembles plasmid contigs from bacterial and metagenomic sequencing data to enable analysis of plasmid-mediated antimicrobial resistance and horizontal gene transfer.

Key Features:

• Plasmid identification: Uses a curated database of known plasmid-associated genes to detect plasmid contigs within assemblies.
• Chromosome–plasmid discrimination: Distinguishes chromosomal from plasmid contigs in complex metagenomic datasets.
• Contig binning: Groups identified plasmid contigs into bins corresponding to individual plasmids.
• Greedy assembly algorithm: Reconstructs plasmid sequences from fragmented contigs using an efficient greedy assembly approach.
• Hybrid strategy: Combines sequence similarity searches against known plasmid genes with de novo assembly techniques to balance sensitivity and specificity.
• Benchmarking: Tested on a large sample of bacterial datasets with reported improved performance relative to existing tools.

Scientific Applications:

• Antimicrobial resistance surveillance: Enables identification and reconstruction of plasmids carrying antibiotic resistance genes for tracking resistance dissemination.
• Horizontal gene transfer studies: Facilitates analysis of plasmid-mediated gene transfer between bacteria.
• Microbial genomics: Supports reconstruction of plasmid complements within bacterial genomes and metagenomes.
• Evolutionary and ecological studies: Provides plasmid-level data relevant to bacterial evolution, adaptation, and ecology.
• Public health research: Supplies plasmid sequence information useful for investigations of clinically relevant resistance and virulence traits.

Methodology:

Performs sequence similarity searches against a curated database of known plasmid genes to identify plasmid contigs, bins contigs into individual plasmids, and reconstructs plasmid sequences using a greedy assembly algorithm within a hybrid framework that integrates similarity-based and de novo assembly techniques.