Justin Chu

ntsm detects sample swaps in heterogeneous sequencing data without alignment, using k-mer variants and coverage information to improve QC efficiency.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

ntHits identifies repeat elements in genomics data using a streaming algorithm, efficiently detecting repetitive k-mers with high accuracy and low resource usage.

RNA-Bloom is a de novo RNA-seq assembler for scRNA-seq data that reconstructs cell-specific isoforms and detects gene fusions, outperforming bulk RNA-seq methods.

ntJoin improves genome assemblies using reference sequences through a lightweight graph-based method, achieving faster and more memory-efficient results than existing tools.

Tigmint corrects genome assembly errors using linked reads from long molecules, improving assembly contiguity and reducing misassemblies.

The paper introduces a multi-index Bloom filter for alignment-free sequence classification, showing improved sensitivity and efficiency over existing methods in read binning and taxonomic assignment.

ARKS improves human genome assemblies using linked read kmers, achieving five-fold better contiguity than baseline methods.

ARCS uses Chromium linked read barcoding information to improve draft genome contiguity, increasing contiguity six-fold with moderate coverage.

The paper reviews and benchmarks overlap detection tools for error-prone long reads, evaluating their performance, efficiency, and scalability.

ABySS 2.0 improves genome assembly efficiency using Bloom filters, achieving high contiguity with reduced memory usage.

NanoSim simulates nanopore sequencing reads with ONT-specific characteristics, enabling testing and development as the technology evolves.