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 …

Metagenome assembly is one of the most useful steps in shotgun metagenomics, but it is also one of the most frustrating. You may start with millions of high-quality reads, …