RepARK

RepARK assembles repetitive motifs de novo from abundant k-mers in next-generation sequencing (NGS) whole-genome shotgun (WGS) reads to generate repeat libraries for identification and analysis of repetitive elements and transposable elements.

Key Features:

• Reference-independent assembly: Assembles repeats directly from sequencing data without requiring a reference genome.
• Efficiency and speed: Runs substantially faster than established methods for generating repeat libraries, enabling large-scale analyses.
• Comprehensive repeat libraries: Produces libraries predominantly composed of repetitive motifs, offering more complete representation than traditional approaches.
• High annotation accuracy: Generated repeat libraries are annotated using TEclass for transposable element classification.
• Applicability to complex genomes: Applicable to model organisms such as Drosophila melanogaster and to larger genomes including the human genome.
• Diagnostic utility: Identifies repetitive sequences that may represent contamination in NGS datasets.

Scientific Applications:

• Genomic research: Facilitates analysis of repeat elements to study genome structure and function.
• Transposable element studies: Provides libraries and annotations for investigating composition and distribution of transposable elements across species.
• Quality control in NGS data: Assists in detecting and mitigating contamination from repetitive sequences in sequencing datasets.

Methodology:

Assembles repetitive motifs directly from abundant k-mers in WGS reads, annotates the resulting repeat libraries using TEclass, and validates performance on simulated and real Drosophila melanogaster NGS data.