Selecting the most suitable pipeline or tool will be dependent on a number of factors including: Your target species and quality of data Some bioinformatic pipelines/software may work better for a particular species based on their unique features (e.g., genome size, repeat complexity, ploidy, etc.) or based on the quality of data (e.g., scaffold length, short reads versus long reads, etc.). While software installation is sometimes provided as a service for some shared HPC platforms, understanding the basics of software installation is useful in helping you troubleshoot any installation-based errors and identify which software you can likely install locally yourself (i.e., without requiring root user privileges). Common software installation methods for bioinformatics tools Package managers APT (Advanced Package Tool) (https://www.debian.org/doc/manuals/apt-guide/index.en.html) is a package manager that is often already installed by default on many Debian distributions and enables very simple installation of available tools. This feature makes conda extremely useful, particularly for bioinformatics software where different pipelines may utilise the same tools but require different versions of a particular tool. [Extracted from the article]