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In-silico PCR and variant primer design
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.gitignore dicey base Jan 14, 2019
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Installing dicey

The easiest way to get Dicey is to download a statically linked binary from the Dicey release page or to download Dicey from Bioconda. Building from source is also possible:

apt-get install -y build-essential g++ cmake zlib1g-dev libbz2-dev liblzma-dev libboost-all-dev

git clone --recursive

cd dicey/

make all

make install

This will generate the binary bin/dicey.

Sequence search in an indexed reference genome

Searching a large reference genome requires a pre-built index on a bgzip compressed genome.

dicey index -o hg19.fa.fm9 hg19.fa.gz

samtools faidx hg19.fa.gz

The indexing step is only required once. You can then search nucleotide sequences at a user-defined edit or hamming distance.

dicey hunt -g hg19.fa.gz TCTCTGCACACACGTTGT | python scripts/

You can also redirect the output in JSON format to a file.

dicey hunt -g hg19.fa.gz -o out.json.gz TCTCTGCACACACGTTGT

In-silico PCR for a set of primers

Dicey can search for multiple primer pairs, show off-target products and determine PCR amplicons.


dicey search -c 45 -g hg19.fa.gz primers.fa | python scripts/

The default output is a JSON file that can also be stored in a file.

dicey search -c 45 -o out.json.gz -g hg19.fa.gz primers.fa


  • Dicey cannot find the primer3 config directory
    The primer3 config directory is included in the repository. Just clone the repository git clone and then use the cloned config directory dicey search -i dicey/src/primer3_config/ -g hg19.fa.gz primers.fa.

  • The script is not found
    The python script is included in the repository. Just clone the repository git clone and then you will find the script in the ./scripts/ subdirectory.


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