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krater

https://github.com/mahajrod/krater

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: mahajrod
  • Language: Python
  • Default Branch: master
  • Size: 1.53 MB
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 2
  • Open Issues: 0
  • Releases: 6
Created almost 10 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.md

DOI

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

Owner

  • Name: Sergei Kliver
  • Login: mahajrod
  • Kind: user

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 189
  • Total Committers: 3
  • Avg Commits per committer: 63.0
  • Development Distribution Score (DDS): 0.037
Past Year
  • Commits: 20
  • Committers: 1
  • Avg Commits per committer: 20.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
mahajrod m****d@g****m 182
mahajrod z****2 6
Сергей Кливер s****r@m****u 1
Committer Domains (Top 20 + Academic)
mcb.nsc.ru: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • lowks (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 113 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 33
  • Total maintainers: 1
pypi.org: krater
  • Versions: 33
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 113 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 19.1%
Average: 20.0%
Downloads: 21.4%
Dependent repos count: 21.7%
Stargazers count: 27.8%
Maintainers (1)
mahajrod
Last synced: 12 months ago

Dependencies

setup.py pypi
  • biopython *
  • matplotlib *
  • numpy *
  • routoolpa *
  • scipy *