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        "description": "# KrATER (K-mer Analysis Tool Easy to Run)\n\nI. Requirements\n\n    1. Python libraries:\n        Matplotlib\n        Numpy\n        Scipy\n        \n    2. Jellyfish 2\n\nII. Installation\n\n    1. Install requirements \n        - install jellyfish 2.x.x  from http://www.genome.umd.edu/jellyfish.html\n    \n        - install python libraries(not necessary if you going to install KrATER via pip)\n            - run following command for global installation\n        \n                sudo pip install matplotlib numpy scipy \n            \n            - or following command for local installation if you don't have root permissions\n        \n                pip install --user matplotlib numpy scipy\n            \n    2. Install KrATER\n        Variant 1: install using pip\n        \n           - run following command for global installation\n           \n                sudo pip install krater\n           \n           - run following commands for local installation\n                \n                pip install --user krater\n                \n              Then add ~/.local/bin in your PATH variable\n              \n                cat \"PATH=\\${PATH}:~/.local/bin/\" >> ~/.profile\n                cat \"PATH=\\${PATH}:~/.local/bin/\" >> ~/.bashrc\n                \n              Load updated PATH variable\n              \n                source ~/.profile\n            \n        Variant 2: install from source code with root permissions\n        \n            git clone https://github.com/mahajrod/krater\n            cd krater\n            python setup.py build\n            sudo python setup.py install\n        \n        \n        Variant 3: install from source code without root permissions\n        \n            Get KRATER\n                git clone https://github.com/mahajrod/krater\n        \n            Add following strings to ~/.profile and ~/.bashrc (create files if absent). Don't forget to replace <KRATER_DIR> with actual path\n            \n                PYTHONPATH=${PYTHONPATH}:<KRATER_DIR>\n                PATH=${PATH}:<KRATER_DIR>\n                export PYTHONPATH\n                export PATH\n                \n            Run in terminal\n                source ~/.profile\n            \n    \nIII. RUN\n\n    1. If input file/files is/are fastq:\n    \n        Typical usage:\n            draw_kmer_distribution_from_fastq.py -m 23  -t ${THREAD_NUMBER} -b -s 30G -e png -o ${OUTPUT_PREFIX} -i {COMMA_SEPARATED_LIST_OF_FASTQ_FILES} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE}  -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE}\n        \n        Parameter description:\n        \n    2. If input file is jellyfish database\n        \n        Typical usage:\n            draw_kmer_distribution_from_jellyfish_database.py -i ${JELLYFISH_DATABASE}  -o ${OUTPUT_PREFIX} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -e png\n        \n    2. If input file is histogram file produced by Jellyfish:\n    \n        Typical usage\n            draw_kmer_distribution_from_histo.py  -i ${JELLYFISH_HISTO_FILE}  -o ${OUTPUT_PREFIX} -w ${MINIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -g ${MAXIMUM_COVERAGE_LIMIT_FOR_NON_LOG_PICTURE} -e png\n        \n        Parameter_description:",
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