Software

  1. R Project, Berkeley CRAN
    Install from the website

  2. RStudio
    Install from the website

  3. R packages
    • tidyr, install.packages(“tidyr”, repos=’http://cran.us.r-project.org’)
    • json, install.packages(“json”, repos=’http://cran.us.r-project.org’)
  4. Anaconda3
    Install from website

  5. htstream
    follow instructions here

  6. bwa

    conda install bwa

  7. freebayes

    conda install -c bioconda freebayes

  8. bcftools conda install -c bioconda bcftools

  9. snpeff

    conda install -c bioconda snpeff