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        "author": "Liam McIntyre",
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        "description": "# Screen assemblies\n\nPipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. Generates multiple CSVs and plots that describe which genes are present and how variable their sequence is. Can use DNA or protein query sequences (GOIs) and DNA contigs/fastas or protein fastas as database (db) to search in. \n\n## Getting Started\n\nYou need one fasta file with all GOIs as the query and a folder with db contigs/fastas. Db files can only have one '.' in the name (i.e., sample_1.fa NOT sample.1.fa) \n\n### Prerequisites\n\n#### Required\n\nPython 3\n\nCommand line blast\n\nftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/\n\n#### Optional\n\nClustal Omega\n\nhttp://www.clustal.org/omega/\n\nIQtree\n\nhttp://www.iqtree.org/doc/Quickstart\n\n### Installing\n\npip3 install --user screen_assembly\n\nMake sure screen_assembly3.py is in you PATH\n\nIf tkinter is missing, do 'sudo apt-get install python3-tk' (on Ubuntu)\n\n### Check for updates\n\npip3 install --user screen_assembly\n\n## Running the tests\n\nOnce screen_assembly3.py is in your PATH type screen_assembly3.py -h . If you have all dependencies then the help menu will display. Otherwise read the erorr and install whichever dependency is missing.\n\n## Running the program\n\nPlease see the WIKI\n\n## Authors\n\n* **Liam McIntyre** - https://github.com/shimbalama/\n\n## License\n\nThis project is licensed under the MIT License - see the LICENSE https://github.com/shimbalama/screen_assembly/blob/master/LICENSE file for details\n\n## Acknowledgments\n\n* Mark Davies lab and Jake for testing\n\n\n\n",
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