LR_Gapcloser

LR_Gapcloser closes gaps in genome assemblies using long reads from third-generation sequencing (TGS) platforms, including public datasets such as NCBI SRA, to improve assembly contiguity and completeness.

Key Features:

• Utilization of Long Reads: Uses long reads from third-generation sequencing (TGS) platforms, including datasets from NCBI SRA, to bridge gaps that short-read methods cannot resolve.
• Efficient and Fast Processing: Implements algorithms aimed at reducing runtime and memory usage compared with existing gap-closure tools.
• High Performance on Diverse Gap Types: Operates on de novo assembled gaps, repeat-derived gaps, and real-world genomic gaps with reduced error rates and improved speed and memory efficiency.
• Improved Contiguity Metrics: Increases contig N50, exemplified by improving the human CHM1 assembly contig N50 from 143 kb to 19 Mb (132-fold increase).
• Applicability Across Genomes: Applies to large, complex, and repeat-rich genomes, demonstrated by a 40% increase in contig N50 for Triticum urartu.
• Integration with Hybrid Assembly Strategies: Integrates with hybrid strategies combining TGS-based and NGS-based assemblers to enhance contiguity and correctness.
• BWA alignment support: Aligns reads using the BWA mem algorithm and includes a pre-compiled BWA package for alignment.

Scientific Applications:

• Genome assembly finishing: Closes gaps to improve contiguity and completeness in de novo and reference-guided genome assemblies.
• Human genomics: Applied to human assemblies such as CHM1 to substantially increase contig N50 and reduce assembly gaps.
• Plant genomics: Used on plant genomes including Triticum urartu to improve contiguity in large, repeat-rich genomes.
• Hybrid assembly workflows: Employed within hybrid TGS/NGS assembly pipelines to improve correctness and overall assembly contiguity.

Methodology:

Long reads are fragmented and aligned to existing scaffolds using BWA mem; alignments are analyzed to identify bridging sequences that span gaps, and those sequences are used to fill the gaps.