Metagenome-assembled genomes, or MAGs, are one of the most useful outputs of shotgun metagenomics. Instead of only asking which organisms are present, MAGs allow researchers to reconstruct draft genomes …

Taxonomic profiling is one of the most common tasks in shotgun metagenomics. After sequencing a microbiome or environmental sample, one of the first questions is usually simple: Which organisms …

DESeq2 is one of the most widely used tools for differential gene expression analysis in RNA-seq experiments. It is powerful, well documented, and suitable for many standard bulk RNA-seq …