ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing.

Area of Science:

• Genomics
• Bioinformatics
• Microbial Genetics

Background:

• Structural variations are crucial for bacterial genome adaptation and antibiotic resistance.
• Detecting small rearrangements in bacterial genomes is challenging.
• Existing tools are often designed for eukaryotic genomes or lack short-read support.

Purpose of the Study:

• To develop a robust workflow for structural variation detection in bacterial genomes using short-read sequencing data.
• To improve detection performance and reliability by integrating multiple detection tools.
• To address the gap in available tools for bacterial structural variation analysis on short-read platforms.

Main Methods:

• Developed ProcaryaSV, an open-source bioinformatics pipeline.
• Integrated quality control, trimming, and alignment steps.
• Incorporated multiple structural variation detection tools and an in-house merging algorithm.

Main Results:

• ProcaryaSV effectively detects structural variations in bacterial isolates from paired-end short reads.
• The pipeline demonstrates improved detection performance compared to single-tool approaches.
• ProcaryaSV is a reproducible and user-friendly tool for bacterial genome analysis.

Conclusions:

• ProcaryaSV offers an integrative approach for bacterial structural variation detection.
• The pipeline is easily installable and usable on Linux systems.
• ProcaryaSV is publicly available on GitHub, promoting open science and accessibility.