Installing dicey

Dicey is available as a Bioconda package, as a pre-compiled statically linked binary from Dicey's github release page, as a singularity container SIF file or as a minimal Docker container.

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

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

cd dicey/

make all

make install

This will generate the binary bin/dicey.

Running Dicey

dicey -h

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

Pre-built genome indices for commonly used reference genomes are available for download here.

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

Padlock probe design

Dicey can design padlock probes for imaging mRNA in single cells. You need to download an indexed reference genome and a matching GTF file, e.g., for GRCh38:

wget http://ftp.ensembl.org/pub/release-107/gtf/homo_sapiens/Homo_sapiens.GRCh38.107.gtf.gz

With these files, you can then design padlock probes for a given gene using

dicey padlock -g Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz -t Homo_sapiens.GRCh38.107.gtf.gz -b data/bar.fa.gz ENSG00000136997

Graphical user interface

You can search primers interactively using our web application silica.

FAQ

• Dicey cannot find the primer3 config directory
  The primer3 config directory is included in the repository. Just clone the repository git clone --recursive 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 --recursive https://github.com/gear-genomics/dicey.git and then you will find the script in the ./scripts/ subdirectory.

Citation

Dicey is part of the GEAR genomics framework which is described in the below publication.

Rausch, T., Fritz, M.H., Untergasser, A. and Benes, V.
Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.
BMC Genomics 21, 230 (2020).
https://doi.org/10.1186/s12864-020-6635-8

License

Dicey is distributed under the GPL license. Consult the accompanying LICENSE file for more details.