GapBlaster-A Graphical Gap Filler for Prokaryote Genomes

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Next-Generation Sequencing (NGS) has led to a surge in available genome data.
• Genome assembly and gap filling are crucial but challenging steps in genomic analysis.
• Complete genomes are essential for downstream analyses like comparative genomics.

Purpose of the Study:

• To introduce GapBlaster, a novel graphical application for evaluating and closing gaps in genome assemblies.
• To provide a user-friendly tool that facilitates manual curation of genome gaps.

Main Methods:

• GapBlaster utilizes contigs from genome assembly to align against a draft genome/scaffold.
• The software employs BLAST or Mummer for gap closure analysis.
• Identified contig alignments extending through gaps are presented via a graphical interface for user evaluation.

Main Results:

• GapBlaster offers significant improvements over existing software for gap filling.
• The application provides a graphical interface, enhancing manual curation of gaps.
• The software is freely available with user guides and test datasets.

Conclusions:

• GapBlaster effectively addresses the challenge of gap filling in genome assembly.
• The tool's graphical interface supports efficient manual curation, leading to more complete genomes.
• GapBlaster is a valuable resource for researchers in genomics and bioinformatics.