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OOD-FISH v0.0.2

Orthogonal Oligo Design for Fluorescence In Situ Hybridization (OOD-FISH) is a pipeline for the identification of oligonucleotide sequences that do not hybridize to a reference genome of interest. Such orthogonal oligonucleotides can easily be used as barcodes for PCR or similar protocols.

Read the documentation for more details.


  1. Clone the git repository locally.
git clone
cd ood-fish
  1. Install R dependencies.
for ( p in c("argparser", "data.table", "parallel", "readr") )
    if ( !require(p, character.only = T) )
  1. Compile if needed.
gcc src/dfeCalc.c -o src/dfeCalc
  1. Install PMC algorithm following the instructions here.


More details on how to run OOD-FISH are available in the documentation.


We welcome any contributions to ood-fish. Please, refer to the contribution guidelines if this is your first time contributing! Also, check out our code of conduct.


MIT License
Copyright (c) 2017-2018 Gabriele Girelli