KrATER (K-mer Analysis Tool Easy to Run)

I. Requirements

1. Python libraries:
    Matplotlib
    Numpy
    Scipy
    
    
2. Jellyfish 2
3. Modified genomescope2

II. Installation

0. Fast way
    - install jellyfish 2.x.x  from http://www.genome.umd.edu/jellyfish.html
    
    - sudo pip install krater
    

1. Install requirements 
    - install jellyfish 2.x.x  from http://www.genome.umd.edu/jellyfish.html

    - install python libraries(not necessary if you going to install KrATER via pip)
        - run following command for global installation
    
            sudo pip install matplotlib numpy matplotlib
        
        - or following command for local installation if you don't have root permissions
    
            pip install --user matplotlib numpy matplotlib
    
    - install modified Genomescope2 from https://github.com/mahajrod/genomescope2.0
    
    
2. Install KrATER
    Use variant 3 to install newest version of KrATER
    Variant 1: install using pip (old version)
    
       - run following command for global installation
       
            sudo pip install krater
       
       - run following commands for local installation
            
            pip install --user krater
            
          Then add ~/.local/bin in your PATH variable
          
            cat "PATH=\${PATH}:~/.local/bin/" >> ~/.profile
            cat "PATH=\${PATH}:~/.local/bin/" >> ~/.bashrc
            
          Load updated PATH variable
          
            source ~/.profile
        
    Variant 2: install from source code with root permissions
    
        git clone https://github.com/mahajrod/krater
        cd krater
        python setup.py build
        sudo python setup.py install
    
    
    Variant 3: install from source code without root permissions
    
        Get KRATER
            git clone https://github.com/mahajrod/krater
    
        Add following strings to ~/.profile and ~/.bashrc (create files if absent). Don't forget to replace <KRATER_DIR> with actual path
        
            PYTHONPATH=${PYTHONPATH}:<KRATER_DIR>
            PATH=${PATH}:<KRATER_DIR>
            export PYTHONPATH
            export PATH
            
        Run in terminal
            source ~/.profile

III. RUN

1. If input file/files is/are fastq:

    Typical usage:
        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}
    
    
2. If input file is jellyfish database
    
    Typical usage:
        draw_kmer_distribution_from_jf_db.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
    
2. If input file is histogram file produced by Jellyfish:

    Typical usage
        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