ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes

Area of Science:

• Genomics
• Bioinformatics

Background:

• Genome assembly from sequencing reads often results in fragmented contigs and scaffolds.
• Achieving a complete genome sequence is a challenging but crucial step in genomic analysis.

Purpose of the Study:

• To introduce ContigPolishing, a user-friendly computational tool designed to improve prokaryotic genome assembly.
• To address the need for robust and simple solutions in genome assembly and polishing.

Main Methods:

• ContigPolishing utilizes an integrated database for resumiable processing.
• The tool was validated using 90 NCBI datasets and raw SRA reads.
• It extends contigs by analyzing flank similarity to improve assembly contiguity.

Main Results:

• ContigPolishing demonstrated improved assembly contiguity, evidenced by increased N50 and improved L50 values.
• The number of contigs was reduced, and draft genomes were successfully upgraded to complete genomes in some instances.
• Validation on diverse datasets confirmed the tool's efficiency in prokaryotic genome assembly.

Conclusions:

• ContigPolishing offers a robust and intuitive solution for enhancing prokaryotic genome assembly.
• The tool effectively improves genome contiguity and aids in achieving complete genome sequences.
• Its integrated database and validation results highlight its practical utility in bioinformatics workflows.