Metadata-Version: 1.0
Name: KrATER
Version: 0.12
Summary: UNKNOWN
Home-page: https://github.com/mahajrod/KRATER
Author: Sergei F. Kliver
Author-email: mahajrod@gmail.com
License: UNKNOWN
Description: # KrATER (K-mer Analysis Tool ER)
        
        I. Requirements
        
            1. Python libraries:
                Matplotlib
                Numpy
                Scipy
                
            2. Jellyfish 2
        
        II. Installation
        
            1. Install requirements
                - run following command for global installation
                    sudo pip install matplotlib numpy scipy 
                - or following command for local installation if you don't have root permissions
                    pip install --user matplotlib numpy scipy
        
            2. Install KrATER
                Variant 1: install using pip
                
                        TODO: add to pip
                    
                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 installation
                
                    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>
                        export PYTHONPATH
            
                    Run in terminal
                        source ~/.profile
                    
            
        III. RUN
        
            1. If nput file/files is/are fastq:
            
                Typical usage:
                    <path to KRATER dir>/scripts/kmer/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}
                
                Parameter description:
                    
                
            2. If input file is histogram file produced by jellyfish:
            
                <path to KRATER dir>/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
                
                Parameter_description:
                
Platform: UNKNOWN
