Dependencies

Running the full processing pipeline – from the server setup to the analysis tutorial – requires the following R packages:

1. neonUtilities
2. dplyr
3. tibble
4. dada2
5. ShortRead
6. Biostrings
7. phyloseq
8. ggplot2
9. geoNEON
10. R.utils
11. vegan (Only required if using the rarecurve() function in test_dada2_params.R
12. plyr
13. utils

Some of these packages cannot be installed using install.packages() and must instead be downloaded from Bioconductor.

You will also need to install cutadapt to run 01a_dada2_worfklow_its.R or 01b_dada2_workflow_16s.R. Installation instructions can be found here. Once installed, change the CUTADAPT_PATH variable in params.R to match the location of the cutadapt command on your system.

Lastly, you will need to install the latest General FASTA Release of the UNITE database for taxonomy assignment of ITS sequences, available here. Once installed, change the UNITED_DB_PATH variable in params.R to match the location of the FASTA file on your system.