{"repo":"epigen/fetch_ngs","free":true,"listed":false,"github":"https://github.com/epigen/fetch_ngs","clone":"git clone https://github.com/epigen/fetch_ngs.git","description":"Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.","language":"Python","stars":47,"topics":["bam","database","fastq","genomics","next-generation-sequencing","ngs","repository"],"license":"MIT","category":"databases-storage","readme_excerpt":"Fetch Public Sequencing Data and Metadata Using iSeq A Snakemake 8 workflow to fetch (download) and process public sequencing data and metadata from GSA , SRA , ENA , GEO and DDBJ databases using iSeq. [!NOTE] This workflow adheres to the module specifications of MrBiomics, an effort to augment research by modularizing (biomedical) data science. For more details, instructions, and modules check out the project's repository. ⭐️ Star and share modules you find valuable 📤 - help others discover them, and guide our future work! [!IMPORTANT] If you use this workflow in a publication, please don't forget to give credit to the authors by citing it using this DOI 10.5281/zenodo.15005419. 🖋️ Authors - Stephan Reichl - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies. Software Reference (DOI) :---: :---: iSeq https://github.com/BioOmics/iSeq pandas https://doi.org/10.5281/zenodo.3509134 Picard https://broadinstitute.github.io/picard/ Snakemake https://doi.org/10.12688/f1000research.29032.2 🔬 Methods This is a template for the Methods section of a scientific publication and is intended to serve as a starting point. Only retain paragraphs relevant to your analysis. References [ref] to the respective publications are curated in the software table above. Versions (ver) have to be read out from the respective conda environment specifications ( workflow/envs/ .yaml file ) or post-execution in the result directory ( {module}","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/fetch_ngs/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}