quickmerge

quickmerge improves genome assembly contiguity by integrating long-read sequencing data from Pacific Biosciences and Oxford Nanopore to reveal structural variants and support comprehensive variant discovery.

Key Features:

• Integration of Long Reads: Leverages long reads (>1 kilobase or ≥30× coverage) to increase assembly contiguity and completeness.
• Hybrid Assembly Compatibility: Supports hybrid assemblies that combine long reads with Illumina short reads to utilize complementary accuracy and read length.
• Cost-Effective High-Quality Assemblies: Enables high-quality de novo assemblies using inexpensive paired reads and scaffolding approaches such as optical map technology to approach reference-level contiguity.
• Comprehensive Variant Discovery: Detects large-scale structural variants (SVs), including long terminal repeat (LTR) transposable element insertions and duplications affecting genes.

Scientific Applications:

• Structural Variant Discovery: Identification of large-scale SVs, including LTR insertions and duplications that impact genes involved in development, behavior, and metabolism.
• De novo Genome Assembly: Generation of highly contiguous de novo assemblies for resequencing and reference improvement.
• Functional Genomics and Phenotype Association: Improved assembly contiguity enables discovery of variants linked to phenotypes and disease-related genetic variation.
• Genome Evolution Studies: Characterization of genome architecture and dynamics through detection of transposable element activity and structural changes.

Methodology:

Resequencing of reference genomes using long-read technologies followed by integration of paired reads and scaffolding with optical map data.