Important: This page is only meant for Linux users. If you are using Windows and WSL, please see Windows Subsystem For Linux.

SeqSphere uses some bioinformatic tools that are not deployed together with the SeqSphere installation. Instead, they must be installed once for each Linux user. The installation can be automatically performed using the SeqSphere menu Help | Check Bioinformatic Tools.

This function installs the latest Miniconda version in the user's home directory (folder miniconda3/), if conda is not already found. After this, it installs the following tools as separate conda environments:

• iVar (SARS-CoV-2 tiled amplicon raw reads processing)
• SISTR (S. enterica geno-serotyping)
• MOB-suite (chromosome and plasmids detection)
• MobileElementFinder
• FastANI (whole genome average nucleotide identity)

On some Linux distributions (e.g. Ubuntu 22.04) this installation also required to run the SPAdes assembler, as it assures the correct python version. Alternatively, the debian package python-is-python3 can be installed.

The installation of miniconda and of the bioinformatic tools can alternatively by done manually by calling the two bash script files in installation folder RidomSeqSphere/ext/install/.