https://github.com/gear-genomics/dicey
In-silico PCR, primer design and padlock design for in-situ sequencing
https://github.com/gear-genomics/dicey
amplicon amplicon-sequencing gear-genomics in-silico in-situ-sequencing padlock pcr primer primer-design sanger-sequencing
Last synced: 17 days ago
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In-silico PCR, primer design and padlock design for in-situ sequencing
- Host: GitHub
- URL: https://github.com/gear-genomics/dicey
- Owner: gear-genomics
- License: gpl-3.0
- Created: 2019-01-14T10:52:36.000Z (about 7 years ago)
- Default Branch: main
- Last Pushed: 2026-01-12T11:23:46.000Z (2 months ago)
- Last Synced: 2026-01-14T14:49:32.758Z (2 months ago)
- Topics: amplicon, amplicon-sequencing, gear-genomics, in-silico, in-situ-sequencing, padlock, pcr, primer, primer-design, sanger-sequencing
- Language: C++
- Homepage: https://www.gear-genomics.com/
- Size: 406 KB
- Stars: 53
- Watchers: 4
- Forks: 3
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Authors: AUTHORS
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README
[](http://bioconda.github.io/recipes/dicey/README.html)
[](https://anaconda.org/bioconda/dicey)
[](https://github.com/gear-genomics/dicey/actions)
[](https://hub.docker.com/r/geargenomics/dicey/)
[](https://github.com/gear-genomics/dicey/blob/master/LICENSE)
[](https://github.com/gear-genomics/dicey/releases)
## Installing dicey
Dicey is available as a [Bioconda package](https://anaconda.org/bioconda/dicey), as a pre-compiled statically linked binary from [Dicey's github release page](https://github.com/gear-genomics/dicey/releases), as a singularity container [SIF file](https://github.com/gear-genomics/dicey/releases) or as a minimal [Docker container](https://hub.docker.com/r/geargenomics/dicey/).
`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](https://gear-genomics.embl.de/data/tracy/).
## 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](https://gear-genomics.embl.de/data/tracy/) 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](https://www.gear-genomics.com/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](https://www.gear-genomics.com) 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](https://doi.org/10.1186/s12864-020-6635-8)
## License
Dicey is distributed under the GPL license. Consult the accompanying [LICENSE](https://github.com/gear-genomics/dicey/blob/master/LICENSE) file for more details.