Lauren Coombe

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

The paper introduces Stash, a hash-based data structure for detecting genome misassemblies using Pacbio HiFi reads, showing it reduces misassemblies in human genome assemblies.

The paper introduces triAMPh, a framework for predicting pathogen-specific antimicrobial peptide activity using biological large language models, showing it matches or outperforms existing methods.

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

The paper compares self-declared and genome-inferred ancestry in 10,250 HostSeq participants, finding high concordance for some groups and lower for others, highlighting the complexity of admixture and the need for complementary approaches.

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

The paper identifies novel antimicrobial peptides from the UniProtKB/Swiss-Prot database using AMPlify, prioritizing 40 for chicken applications and testing 38 for antimicrobial activity.

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

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

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

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

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

The paper sequences and assembles the largest complete mitochondrial genome of a gymnosperm, Sitka spruce, revealing a complex multipartite structure.

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

ntEdit is a genome polishing tool that efficiently corrects base errors in genomic sequences across various species and coverage levels.

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

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.

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