TELLBASE: a novel tool of TELL-seq barcode-assisted scaffold assembler for bacterial genomes

Area of Science:

• Genomics and Bioinformatics
• Microbial Genomics
• Sequencing Technology Applications

Background:

• Transposase enzyme linked long-read sequencing (TELL-seq) offers advantages for whole-genome sequencing (WGS) due to barcode-linked reads and efficient genomic information capture.
• Existing assembly algorithms struggle to fully utilize TELL-seq data for megabase-scale bacterial genome and plasmid assembly.

Purpose of the Study:

• To develop a de novo genome assembler, TELLBASE, specifically designed for bacterial genomes using TELL-seq data.
• To evaluate TELLBASE's performance in assembling bacterial chromosomes and identifying plasmids.

Main Methods:

• Development of TELLBASE, a novel assembler leveraging TELL-seq barcode-linked reads.
• Application of TELLBASE to assemble genomes of diverse bacteria, including Acinetobacter baumannii, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Staphylococcus aureus.
• Comparative analysis against existing TELL-seq assemblers (TuringAssembler, Ariadne).

Main Results:

• TELLBASE successfully generated chromosome-level bacterial genomic sequences and identified plasmids.
• Demonstrated exceptional efficacy in assembling bacterial genomes with high completeness and accuracy.
• Significantly outperformed TuringAssembler and Ariadne in comparative assembly tests.

Conclusions:

• TELLBASE is a highly effective tool for assembling bacterial genomes from TELL-seq data.
• The assembler shows significant potential for refining draft bacterial genomes and advancing microbial genomics research.
• TELLBASE is freely available on GitHub, promoting wider adoption and application.