Rasmus Hansen Kirkegaard

The paper constructs a global genome catalog of 53,501 long-read MAGs from activated sludge, representing 12,047 prokaryotic species and enabling analysis of functional traits and ecological roles in wastewater treatment systems.

Savont improves ASV recovery from long-read amplicon sequencing with high accuracy and lower sequencing depth.

This study shows that Oxford Nanopore Technologies can generate amplicon sequence variants (ASVs) directly from raw reads, enabling high-resolution microbial community profiling without reliance on reference databases.

The paper presents a national study of methanotroph diversity and distribution in Denmark, revealing uncharacterised species as dominant in natural ecosystems and highlighting potential targets for methane mitigation.

Microflora Danica compiles 10,686 shotgun metagenomes and 449 rRNA datasets to create an atlas of Danish environmental microbiomes, revealing hidden homogeneity and novel nitrifiers.

The paper examines microbial metabolic capabilities and spatial distribution along a redox gradient to show that background metabolic differences and spatial partitioning prevent ecological equivalence among microbes.

Nanomotif uses DNA methylation motifs to improve MAG recovery and plasmid host association from metagenomic data.

Dual patterned unique molecular identifiers (UMIs) turn Nanopore or PacBio CCS reads of ~4400 bp rRNA operons into single-molecule consensus sequences with 0.0049% (ONT) or 0.0006% (PacBio) mean error.

ampvis2 unifies 16S amplicon count tables, taxonomy, and sample metadata in one R object, feeding ggplot2 heatmaps at any taxonomic rank and single-call ordination (seven methods).

The paper introduces mmgenome, a toolbox for reproducible genome extraction from metagenomes, integrating binning strategies, visualization, validation, and full reproducibility through Rmarkdown.