Torbjørn Rognes

Benchmarking 16S rRNA gene amplicon analysis in high-diversity microbial communities reveals fundamental trade-offs in clustering and denoising

This study benchmarks 16S rRNA gene analysis pipelines in high-diversity datasets, revealing trade-offs between clustering accuracy, species recovery, and abundance reconstruction.

Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data

VirMake processes shotgun metagenomic data to identify and characterize viral taxa and functions, showing variability in viral genome richness and taxonomy across environments and protocols.

HoCoRT: Host contamination removal tool

HoCoRT removes host contamination from shotgun metagenome sequencing data using multiple methods, finding optimal combinations for accuracy and speed.

MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions

MoDLE is a computational tool that rapidly simulates DNA loop extrusion contact patterns, matching existing methods and Micro-C data with high accuracy.

CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching

CompAIRR rapidly compares adaptive immune receptor repertoires using exact or approximate sequence matching, significantly improving speed and memory efficiency compared to existing methods.

NucBreak: Location of structural errors in a genome assembly by using paired-end Illumina reads

NucBreak detects structural errors in genome assemblies using paired-end Illumina reads, showing high sensitivity and precision compared to existing tools.

NucMerge: Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads

NucMerge improves genome assembly accuracy by integrating alternative assemblies and paired-end Illumina reads, outperforming existing tools in error correction and rearrangement detection.