Dependencies

If you're working on a HPC, it is recommended that you use the provided docker image to run this pipeline instead of manually installing these dependencies onto your device. Click here for Docker/Singularity instructions.

If you're working on your personal computer, we'd suggest using this script to install the R dependencies, and individually installing the Unix dependencies. Change directories into the metabarcoding_QAQC_pipeline directory and run:

Rscript install_dependencies.R

Unix:

• Python v.3.8 https://www.python.org/downloads/
• Cutadapt v.4.2 https://cutadapt.readthedocs.io/en/stable/
• Quarto v.1.3+ https://quarto.org/docs/get-started/
• Pandoc v.3.0.1+ https://pandoc.org

R CRAN:

• tidyverse v.2.2.0 https://www.tidyverse.org
• seqinr v.4.2-23 https://seqinr.r-forge.r-project.org
• digest v.0.6.31 https://cran.r-project.org/web/packages/digest/index.html
• quarto https://cran.r-project.org/web/packages/quarto/index.html
• rmarkdown https://rmarkdown.rstudio.com
• pander https://cran.r-project.org/web/packages/pander/index.html
• pandoc https://cran.r-project.org/web/packages/pandoc/index.html
• ggplot2 https://ggplot2.tidyverse.org
• dplyr https://cran.r-project.org/web/packages/dplyr/index.html
• strex https://cran.r-project.org/web/packages/strex/index.html
• sqldf https://www.rdocumentation.org/packages/sqldf/versions/0.4-11
• knitr https://www.r-project.org/nosvn/pandoc/knitr.html
• rmdformats https://cran.r-project.org/web/packages/rmdformats/readme/README.html
• data.table https://cran.r-project.org/web/packages/data.table/index.html
• filesstrings https://cran.r-project.org/web/packages/filesstrings/index.html

Bioconductor:

• dada2 v.1.26.0 https://benjjneb.github.io/dada2/
• ShortRead v.1.56.1 https://bioconductor.org/packages/release/bioc/html/ShortRead.html
• phyloseq https://joey711.github.io/phyloseq/