Bede Constantinides

The paper introduces K2Rmini, a tool that efficiently filters sequences based on k-mer matches, achieving 2 Gbp/s on a consumer laptop.

This study shows that library preparation methods significantly affect RNA virus detection in clinical metagenomics, with SISPA-based approaches outperforming others in most scenarios.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

This paper evaluates the performance of the gnomonicus tool for predicting antibiotic resistance in Mycobacterium tuberculosis using a diverse testset of 2,663 samples and compares it to TB-Profiler.

Deacon efficiently filters and depletes contaminant sequences from large genomic datasets using a human pangenome index, achieving high accuracy and speed with minimal computational resources.

Hostile is a tool for removing human host sequences from microbial sequencing data, achieving high accuracy in read removal while preserving target microbial sequences.

The paper evaluates metagenomic, 16S rRNA gene, and ultra-plexed PCR-based sequencing methods for taxonomic and AMR gene profiling in polymicrobial samples, finding that AmpliSeq and shotgun metagenomics perform best for resistome profiling.

ReadItAndKeep removes human contamination from SARS-CoV-2 sequencing data efficiently on low-specification laptops.

Flanker clusters gene flanking sequences to identify mobile genetic element patterns associated with antimicrobial resistance genes.