ntHits

ntHits identifies de novo repetitive elements from high-throughput DNA sequencing data to characterize satellites, transposons, gene copies, and segmental duplications that complicate eukaryotic genome assembly and comparisons.

Key Features:

• Streaming Algorithm: ntHits employs a streaming algorithm that uses statistical analysis of k-mer content profiles to identify repeats in large-scale sequencing data.
• k-mer Coverage Histograms: It uses ntCard, a complementary streaming method, to estimate k-mer coverage histograms and detect the long-tail distribution of repetitive k-mers.
• Performance and Efficiency: ntHits identified repeat k-mers in a 96× white spruce sequencing dataset in approximately 12 hours using less than 150 GB of memory, compared to exact methods that require several days and terabytes of memory and disk space.
• Parallelization: ntHits leverages OpenMP for parallel processing and requires a modern compiler such as GCC version 4.2 or greater to utilize this capability.

Scientific Applications:

• Genome Assembly and Comparison: Identification and classification of repetitive elements to improve accuracy of genome assembly and comparisons across species or strains.
• Analysis of Duplications and Rearrangements: Providing insights into repeat content to aid analysis of large-scale duplications and genomic rearrangements.

Methodology:

ntHits generates k-mer coverage histograms from sequencing data using ntCard and analyzes those histograms to detect repetitive k-mers indicative of genomic repeats.