Using Kraken2 & BBDuk to check for contamination in short-read datasets

This tutorial will guide you through: Strategies for cleaning and QCing your data How to install Kraken2, build a database, and use it to “decontaminate” your short reads How to use BBDuk to clean your datasets for more unusual use cases, such as removing mitochondrial or plastid genomes. Before you get started… Kraken2 [1] is […]