This directory is to assign taxonomy to your list of ASVs inferred from each study, using the Silva reference database. It allows to assign taxonomy on a computer cluster instead of running it on your local computer.
Necessary elements:
- Fasta files containing the Silva reference database must be put in the
silva-taxonomic-ref/subdirectory (see README file in the silva-taxonomic-ref subdirectory) - Input ASV tables in the
input/subdirectory with samples as rows and ASV sequences in column names. These input ASV tables should have no chimera and are generated by the scripts01_Dada2-NameDataset.Rmdin each individual dataset subdirectory of analysis-individual - R script to assign taxonomy on all datasets present in the
input/subdirectory =>Rscript_assignTaxonomy_cluster.Ris already provided in this directory, but make sure to change the file paths at the top of the R script!! - Bash script to execute the R script on your computer cluster (recommended to provide at least XXXXX of virtual memory!). Make sure to modify the bash script provided in this directory to fit your cluster.
