Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally resolved reference genome assemblies for over 2,000 species. Tree of Life has at its core multiple teams, each of which is responsible for key components of the "genome engine." One of these teams is the Tree of Life core laboratory, which is responsible for processing tissues across a wide range of species into high-quality, high molecular weight DNA and intact RNA, and preparing tissues for Hi-C. Here, we detail the different workflows we have developed to successfully process a wide variety of species, covering plants, fungi, chordates, protists, arthropods, meiofauna, and other metazoa. We summarise our success rates and describe how to best apply and combine the suite of current protocols, which are all publicly available at https://dx.doi.org/10.17504/protocols.io.8epv5xxy6g1b/v2.