System requirements

FaST requires at least 32 Gb of RAM and a multicore processor with at least 8 cores/16 threads. More threads may marginally speed up the analysis, especially if using a SSD drive. All the currently available public datasets compatible with FaST can be analysed with 32 Gb of RAM.

Software requirements

FaST has been developed to run in a bash shell on Linux OS. FaST currently requires:

  • bedtools v2.30.0 or later

  • samtools v1.19.2 (but any version will likely work as the only samtool invoked by FaST is “samtools view”)

  • STAR v2.7.11a or later

  • spateo-release v1.0.2 (for RNA segmentation only)

  • scanpy v1.10.1 or later

It is advisable to take advantage of the FaST_env.yml file in the data folder to create a dedicated environment.

Installing FaST

Fast comes as a set of bash, Perl and Python scripts. To install it you should simply clone the github repository to a suitable location of your filesystem. Optionally, you can add the /path/to/FaST/scripts/ directory to your PATH evironmental variable. This will allow you to run FaST by just typing FaST

$ FaST -h

instead of

$ /path/to/FaST/scripts/FaST -h

If you choose to run FaST in the dedicated environment, remember activating the environment before running FaST.