Johnathan Wong

biHash: bisulfite-aware recursive nucleotide hashing

biHash is a rolling hash algorithm designed for bisulfite-sequenced data, offering faster hashing by recognizing bisulfite-compatible sequence states.

aaKomp: Alignment-free amino acid k-mer matching for genome completeness assessment at scale

aaKomp provides a fast, memory-efficient, alignment-free method for genome completeness assessment, outperforming existing tools in speed and scalability.

Multi-genome synteny detection using minimizer graph mappings

The paper introduces ntSynt, a tool for detecting multi-genome synteny blocks using minimizer graphs, showing high coverage and efficiency across diverse genomes.

GoldPolish-Target: Targeted long-read genome assembly polishing

GoldPolish-Target polishes targeted regions of genome assemblies, reducing errors and improving accuracy with lower computational demands.

ntRoot: Computational Inference of Human Ancestry at Scale from Genomic Data

ntRoot infers human super-population ancestry from genomic data with high accuracy and efficiency, outperforming traditional methods on large datasets.

GoldRush: A de novo long read genome assembler with linear time complexity

GoldRush is a de novo long read genome assembler with linear time complexity, achieving efficient assembly of large genomes with high contiguity and low memory usage.

aaHash: recursive amino acid sequence hashing

aaHash is a recursive amino acid sequence hashing algorithm that improves speed and sensitivity for protein sequence analysis.

LongStitch: High-quality genome assembly correction and scaffolding using long reads

LongStitch improves draft genome assemblies using long reads, significantly increasing contiguity and accuracy compared to existing methods.

Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation

The paper analyzes APA patterns in 114 cancer-related genes across 33 cancer types to show complex 3 UTR cleavage changes in tumors.