KrATER 2.5

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# KrATER (K-mer Analysis Tool Easy to Run)

1. Requirements

   1. Python libraries:

      Matplotlib Numpy Scipy

      RouToolPa (https://github.com/mahajrod/RouToolPa)

   2. Jellyfish 2

2. Installation

   0. Fast way

      • install jellyfish 2.x.x from http://www.genome.umd.edu/jellyfish.html

      • sudo pip install routoolpa krater

      or

      • pip install –user routoolpa 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 scipy

        • or following command for local installation if you don’t have root permissions

          pip install –user matplotlib numpy scipy

      • install RouToolPa

        From pip with root permission:

        sudo pip install routoolpa

        From pip without root permissions:

        pip install –user routoolpa

        Get RouToolPa

        git clone https://github.com/mahajrod/routoolpa

        Add following strings to ~/.profile and ~/.bashrc (create files if absent). Don’t forget to replace <ROUTOOLPA_DIR> with actual path

        PYTHONPATH=${PYTHONPATH}:<ROUTOOLPA_DIR> PATH=${PATH}:<ROUTOOLPA_DIR> export PYTHONPATH export PATH

        Run in terminal

        source ~/.profile

   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

3. 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}

   Parameter description:

2. If input file is jellyfish database

   Typical usage:

   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

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

   Parameter_description: