gapFinisher

gapFinisher closes gaps in genome assemblies produced by SSPACE-LongRead by using long reads from third-generation sequencing platforms to improve completeness of de novo draft genomes.

Key Features:

• Integration with SSPACE-LongRead: Processes scaffold outputs from SSPACE-LongRead and uses sequence information from long reads generated by third-generation sequencing platforms to close gaps within scaffolds.
• Automated Pipeline: Automates gap-filling steps into a reproducible pipeline without manual intervention.
• Reliability and Correctness: Implements a controlled application of FGAP to prioritize accurate and dependable gap closure.
• Performance and Scalability: Uses a serial design that scales from prokaryotic genomes to larger genomes and has been reported to outperform PBJelly and GMcloser in speed and reliability.
• Platform Compatibility: Executes on standard Linux/UNIX command lines.

Scientific Applications:

• Gap closure in de novo assemblies: Closes unknown sequences in draft genomes and scaffolds produced by SSPACE-LongRead.
• Improved downstream analyses: Increases completeness for gene annotation, comparative genomics, and evolutionary studies by reducing scaffold gaps.
• Applicability across taxa: Applicable to microbial (prokaryotic) genomes and larger plant and animal genome projects.

Methodology:

Processes SSPACE-LongRead scaffold outputs and uses sequence information from long reads to perform gap filling via a controlled application of FGAP following a serial design.