Skip to content
Re-analysis of Singapore metabarcodes
Shell R
Branch: master
Clone or download
Latest commit e84959e Sep 5, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R Small changes for revised version Sep 4, 2019
qiime-scripts Update qiime scripts Sep 5, 2019
.gitattributes 👾 Added .gitattributes Jul 5, 2018
.gitignore Update qiime scripts Sep 5, 2019
README.md Update README.md Sep 5, 2019

README.md

Singapore-metabarcodes

Script and processed data for :

  • Chénard, C., Wijaya, W., Vaulot, D., Lopes dos Santos, A., Martin, P., Kaur, A. & Lauro, F.M. 2019. Spatial and temporal dynamics of microbial communities in equatorial coastal waters. Scientific Reports submitted

Directories

qiime-scripts

  • monsoon_qiime_script.sh : Qiime script to process raw data and do some analyses
  • manifest.csv: list of fastq files
  • metadata.txt: sample list
  • metadata_volatility.txt : data for volatilty analysis

R

  • Metabarcoding_Singapore_phyloseq.Rmd : Script to produce phyloseq files and produce plots (HTML version of Rmd file)
  • monsoonpaper_env_data.csv : environmental metadata
  • Singapore_metadata.xlsx : list of samples and of stations with environmental data
  • Singapore ASV_table.xlsx :
    • Sheet ASV finale: List of ASVs, taxonomic assignations, read number in each sample, and sequence
    • Sheet BLAST: Best BLAST for each eukaryotic ASV
You can’t perform that action at this time.