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In-silico PCR and variant primer design
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README.md

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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 https://github.com/gear-genomics/dicey.git

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/json2txt.py

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.

echo -e ">FGA_f\nGCCCCATAGGTTTTGAACTCA\n>FGA_r\nTGATTTGTCTGTAATTGCCAGC" > primers.fa

dicey search -c 45 -g hg19.fa.gz primers.fa | python scripts/json2txt.py

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

FAQ

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

  • The script json2txt.py is not found
    The json2txt.py python script is included in the repository. Just clone the repository git clone https://github.com/gear-genomics/dicey.git and then you will find the script in the ./scripts/ subdirectory.

Questions

In case of questions feel free to send us an email.

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