Gapfiller

Gapfiller closes gaps in scaffold sequences of de novo genome assemblies by using paired-end reads from next-generation sequencing to improve assembly contiguity and completeness.

Key Features:

• Paired-end read-based gap closure: Uses paired-end reads from next-generation sequencing to fill gaps within scaffold sequences.
• Automated strategy: Implements an automated approach to close gaps in draft assemblies.
• Improved contiguity and completeness: Increases contiguity and completeness of draft genome assemblies.
• Minimal errors introduced: Produces gap closures with only a minimal number of errors introduced during the process.
• Cross-taxa applicability: Has been tested on bacterial and eukaryotic datasets, demonstrating applicability across diverse organisms.
• Reduces additional sequencing needs: Utilizes existing paired-read data to reduce the need for additional wet-lab sequencing for gap closure.

Scientific Applications:

• De novo assembly finishing: Enhances draft de novo genome assemblies to produce more contiguous genomes for downstream analysis.
• Microbial and eukaryotic genomics: Applicable to genome projects for both bacterial and eukaryotic organisms.
• Support for downstream biological analyses: Provides more complete genome sequences for subsequent biological analyses and applications.

Methodology:

Uses paired-end reads from next-generation sequencing to identify and fill gaps within scaffold sequences in an automated manner.