GAPPadder: a sensitive approach for closing gaps on draft genomes with short sequence reads.

Area of Science:

• Genomics
• Bioinformatics

Background:

• Genome assembly requires closing gaps for complete genomes, crucial for annotation and genotyping.
• Existing gap-closing tools often fail to leverage all available sequence data, particularly reads from repeat-related gaps.

Purpose of the Study:

• Introduce GAPPadder, a novel approach for enhanced genome gap closing.
• Improve genome completeness by utilizing previously ignored sequence information.

Main Methods:

• GAPPadder identifies and incorporates sequence reads originating from repeat-related gaps.
• The method utilizes sequence reads with varying insert sizes.
• Employs a two-stage local assembly process for gap sequences.

Main Results:

• GAPPadder closes more gaps compared to established tools like GapCloser, GapFiller, and Sealer.
• Demonstrated effectiveness on bacterial, human, bed bug, and Asian sea bass genomes.
• Achieves efficient time and memory usage.

Conclusions:

• GAPPadder offers a significant advancement in genome gap closing by leveraging repeat-associated reads.
• The tool enhances genome assembly quality and is applicable to various sequencing data types.
• GAPPadder is available as open-source software.