Repo for data generating scripts, paper rmarkdown and other files involved in methods
Contents of the repository:
── README.md
├── SILVA_132_SSURef_tax_silva.fasta
├── docs
│ ├── 2019-Nolan-Waters-focusdb.Rmd # main text of paper
│ ├── 2019-Nolan-Waters-supplementary.Rmd # code and details of analysis
│ ├── DADA2_analysis.Rmd # code for running community analysis
│ ├── figures # location for figures
│ ├── focusdb_references.bib # references
│ ├── blob_SRR2155541 # Blobtools results of potentially contaminated datasets
│ ├── blob_SRR3571775 # //
├── results
│ ├── 2019-12-19-results.tar.gz # seqeunces, etc for organisms studied
│ ├── fast_focusDB_ribo16s.fasta # extracted 16S alleles from --fast mode
│ └── full_focusDB_ribo16s.fasta # extracted 16S alleles from full mode
└── scripts
└── sralist.py # for generating counts per organism of SRAs availabl
The working directory for all the markdown scripts is ./docs/, not the project directory. If using RStudio, you can configure this under your project settings.