KrATER 0.1

UNKNOWN

# KrATER (K-mer Analysis Tool ER)

1. Requirements

   1. Python libraries:

      Matplotlib Numpy Scipy

   2. Jellyfish 2

2. 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

3. 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: