This repository contains code and metadata for the 221014Esv Illumina run. It includes code to i) turn CZID biom files into phyloseq objects (illumina_import_and_datacleaning.Rmd) ii) analyses of the resulting phyloseq objects (Illumina_analysis.RmD) iii) import of kraken2 results and linking kraken2 data with ICTV metadata (Illumina_kraken2_import.Rmd), a
DNA sequences that are analyzed here stem from 12 Illumina samples; gained from aliquots from the same 0.5L wastewater sample, taken from an anonymous wastewater plant.
More information on the sequencing runs can be found here(only accessible for NAO members).
- Turn Simon's R Scripts into Pyhton scripts that can be integrated into Jeff's pipeline
- Automate the download of the updated ICTV table