FaST: Fast analysis of Spatial Transcriptomics

The FaST pipeline allows a quick processing of spatial transcriptomics datasets obtained by repurposing the Illumina flowcells as an RNA capture device. Thus far, several flavours of such protocols have been published including Seqscope, OpenST and Novaseq.

Usage

FaST has a simple command line interface. Through command line three major actions can be performed:

• FaST-map is the command that will take care of processing the first HDMI barcode sequencing output.

• FaST-reference is needed to build on your filesystem a local set of reference files for your model organism.

• FaST will launch the analysis of a single experiment (using the HDMI barcode map generated by FaST-map and the refernce generated by FaST-reference).

Contents

• Installing FaST
  • System requirements
  • Software requirements
  • Installation
• Input data
• FaST-map
  • Usage
    • Command syntax for Illumina (Nova-ST, OpenST, seqscope, Novascope):
    • Command syntax for Stereo-seq (STOmics):
  • Notes on fastq.gz input files
• FaST-reference
  • Usage
  • Notes
• FaST
  • Usage
  • Notes
• Step by step guide to FaST pipeline
  • Step 1: FaST-map
  • Step 2: FaST-reference
  • Step 3: FaST