Home

Awesome

install with bioconda Anaconda-Server Badge C/C++ CI Docker CI GitHub license GitHub Releases

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

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.