corona-fish

This repository provide the code used to design smiFISH probes against SARS-cov-2.

Organization of repository

• covfish: python modules with helper functions.
• data: contains data-sets required for the probe-design.
  • fasta: fasta sequences against fish probes were designed
  • genomes: different genomes for local blast
• docs: folder containing documentation for probe-design workflow, the actual design software Oligostan, and our smFISH protocol.
• workflows: different steps in the analysis workflows, e.g for the probe-design.

Getting started

The provided code uses Python and R.

• For Python, we recommend installing Miniconda with Python: choose Python 3.7 and your operating system.
• For R, we recommend installing R and the free versio of RStudio Desktop.

Creating a dedicated Python environment

Most of the provide code runs under Python.

We recommend creating a dedicated environment to run code in this analysis package.

To create an environment called corona-fish, open an anaconda prompt and type (Confirm with y when asked if you want to proceed (Proceed ([y]/n)?):

conda create --name corona-fish python=3.7

Activate the environment:

conda activate corona-fish

Install code for this package:

• Pip install from the web:

  pip install git+git:https://github.com/muellerflorian/corona-fish

• Or a local pip install for development:

  pip install -e /path/to/package`

Workflow for probe design

For a detailed description of the design process for the probes, please consult the dedicated documentation.