Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

Area of Science:

• Genomics
• Bioinformatics
• Microbial Evolution

Background:

• Complete bacterial genomes are essential for understanding evolution and antimicrobial resistance.
• Hybrid assembly (short- and long-reads) is standard, but small plasmids are often missed.
• Existing long-read assemblers struggle with accuracy and plasmid recovery.

Purpose of the Study:

• Introduce Hybracter, a novel long-read-first assembly tool.
• Enable fast, automatic, and scalable bacterial genome reconstruction.
• Improve the accurate recovery of complete bacterial genomes, including small plasmids.

Main Methods:

• Developed Hybracter, a long-read-first assembly approach.
• Evaluated Hybracter in hybrid and long-read-only modes.
• Compared performance against Unicycler and other assemblers using curated reference genomes.

Main Results:

• Hybracter as a hybrid assembler is more accurate and faster than Unicycler.
• Hybracter as a long-read-only assembler is the most accurate available.
• Both modes demonstrate high accuracy in recovering small plasmids.

Conclusions:

• Hybracter provides a significant advancement in bacterial genome assembly.
• The tool offers a scalable and efficient solution for complete genome reconstruction.
• Hybracter improves the identification of medically significant plasmids.