{"id":37104110,"url":"https://github.com/gear-genomics/dicey","last_synced_at":"2026-02-26T13:01:26.829Z","repository":{"id":63771460,"uuid":"165645217","full_name":"gear-genomics/dicey","owner":"gear-genomics","description":"In-silico PCR, primer design and padlock design for in-situ 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["amplicon","amplicon-sequencing","gear-genomics","in-silico","in-situ-sequencing","padlock","pcr","primer","primer-design","sanger-sequencing"],"created_at":"2026-01-14T12:35:31.943Z","updated_at":"2026-02-26T13:01:26.786Z","avatar_url":"https://github.com/gear-genomics.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/dicey/README.html)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/dicey/badges/downloads.svg)](https://anaconda.org/bioconda/dicey)\n[![C/C++ CI](https://github.com/gear-genomics/dicey/workflows/C/C++%20CI/badge.svg)](https://github.com/gear-genomics/dicey/actions)\n[![Docker CI](https://github.com/gear-genomics/dicey/workflows/Docker%20CI/badge.svg)](https://hub.docker.com/r/geargenomics/dicey/)\n[![GitHub license](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/gear-genomics/dicey/blob/master/LICENSE)\n[![GitHub Releases](https://img.shields.io/github/release/gear-genomics/dicey.svg)](https://github.com/gear-genomics/dicey/releases)\n\n## Installing dicey\n\nDicey 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/).\n\n`apt-get install -y build-essential g++ cmake zlib1g-dev libbz2-dev liblzma-dev libboost-all-dev autoconf`\n\n`git clone --recursive https://github.com/gear-genomics/dicey.git`\n\n`cd dicey/`\n\n`make all`\n\n`make install`\n\nThis will generate the binary `bin/dicey`.\n\n\n## Running Dicey\n\n`dicey -h`\n\n## Sequence search in an indexed reference genome\n\nSearching a large reference genome requires a pre-built index on a bgzip compressed genome.\n\n`dicey index -o hg19.fa.fm9 hg19.fa.gz`\n\n`samtools faidx hg19.fa.gz`\n\nThe indexing step is only required once. You can then search nucleotide sequences at a user-defined edit or hamming distance.\n\n`dicey hunt -g hg19.fa.gz TCTCTGCACACACGTTGT | python scripts/json2txt.py`\n\nYou can also redirect the output in JSON format to a file.\n\n`dicey hunt -g hg19.fa.gz -o out.json.gz TCTCTGCACACACGTTGT`\n\nPre-built genome indices for commonly used reference genomes are available for [download here](https://gear-genomics.embl.de/data/tracy/).\n\n\n## In-silico PCR for a set of primers\n\nDicey can search for multiple primer pairs, show off-target products and determine PCR amplicons.\n\n`echo -e \"\u003eFGA_f\\nGCCCCATAGGTTTTGAACTCA\\n\u003eFGA_r\\nTGATTTGTCTGTAATTGCCAGC\" \u003e primers.fa`\n\n`dicey search -c 45 -g hg19.fa.gz primers.fa | python scripts/json2txt.py`\n\nThe default output is a JSON file that can also be stored in a file.\n\n`dicey search -c 45 -o out.json.gz -g hg19.fa.gz primers.fa`\n\n\n## Padlock probe design\n\nDicey 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:\n\n`wget http://ftp.ensembl.org/pub/release-107/gtf/homo_sapiens/Homo_sapiens.GRCh38.107.gtf.gz`\n\nWith these files, you can then design padlock probes for a given gene using\n\n`dicey padlock -g Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz -t Homo_sapiens.GRCh38.107.gtf.gz -b data/bar.fa.gz ENSG00000136997`\n\n\n## Graphical user interface\n\nYou can search primers interactively using our web application [silica](https://www.gear-genomics.com/silica/).\n\n\n## FAQ\n\n* Dicey cannot find the primer3 config directory    \nThe 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`.\n\n* The script `json2txt.py` is not found     \nThe `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.\n\n\n## Citation\n\nDicey is part of the [GEAR genomics framework](https://www.gear-genomics.com) which is described in the below publication.\n\nRausch, T., Fritz, M.H., Untergasser, A. and Benes, V.         \nTracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.             \nBMC Genomics 21, 230 (2020).             \n[https://doi.org/10.1186/s12864-020-6635-8](https://doi.org/10.1186/s12864-020-6635-8)\n\n\n## License\n\nDicey is distributed under the GPL license. Consult the accompanying [LICENSE](https://github.com/gear-genomics/dicey/blob/master/LICENSE) file for more details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgear-genomics%2Fdicey","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgear-genomics%2Fdicey","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgear-genomics%2Fdicey/lists"}