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.
- Clone the git repository locally.
git clone https://github.com/ggirelli/ood-fish/
cd ood-fish- Install R dependencies.
for ( p in c("argparser", "data.table", "parallel", "readr") )
if ( !require(p, character.only = T) )
install.packages(p)- Compile if needed.
gcc src/dfeCalc.c -o src/dfeCalc- 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