Abstract here
root
├── code
│ ├── 00_setup.ipynb
│ ├── 01_qiime2_part1.html
│ ├── 01_qiime2_part1.ipynb
│ ├── 02_feature_filtering.html
│ ├── 02_feature_filtering.Rmd
│ ├── 03_qiime2_part2.html
│ ├── 03_qiime2_part2.ipynb
│ ├── 04_qiime2R.html
│ ├── 04_qiime2R.Rmd
│ ├── 05_taxonomy_tilapia.html
│ ├── 05_taxonomy_tilapia.Rmd
│ ├── 06_alpha_diversity_tilapia.html
│ ├── 06_alpha_diversity_tilapia.Rmd
│ ├── 07_beta_diversity_tilapia.html
│ ├── 07_beta_diversity_tilapia.Rmd
│ ├── 08_differential_analysis_tilapia.html
│ ├── 08_differential_analysis_tilapia.Rmd
│ ├── 09_taxonomy_perch.html
│ ├── 09_taxonomy_perch.Rmd
│ ├── 10_alpha_diversity_perch.html
│ ├── 10_alpha_diversity_perch.Rmd
│ ├── 11_beta_diversity_perch.html
│ ├── 11_beta_diversity_perch.Rmd
│ ├── 12_differential_analysis_perch.html
│ ├── 12_differential_analysis_perch.Rmd
│ ├── functions
│ │ ├── plot_betadisper.R
│ │ ├── plot_frequency.R
│ │ ├── plot_heatmap.R
│ │ └── plot_prevalence.R
│ └── README.md
├── data
│ ├── raw
│ │ ├── fastq
│ │ ├── qPCR
│ │ └── README.md
│ ├── reference
│ │ ├── silva_132_99_16S.fna
│ │ ├── silva_132_consensus_taxonomy_l7.txt
│ │ ├── sepp-refs-silva-128.qza
│ │ └── README.md
│ ├── intermediate
│ │ ├── filtering
│ │ ├── qiime2
│ │ ├── qiime2R
│ │ ├── permanova
│ │ └── maaslin2
│ └── metadata.tsv
├── result
│ ├── figure
│ │ ├── perch
│ │ └── tilapia
│ └── table
│ ├── perch
│ └── tilapia
├── Kizito_tilapia-perch-microbiota_2021.Rproj
├── LICENSE.md
└── README.md
- Miniconda3 should be located in your HOME directory.
- QIIME2 (2021.4) should be installed within a Miniconda3 environment and named as
qiime2-2021.4.- QIIME2 library: DEICODE (0.2.3) should be installed within the qiime2 conda environment.
- grabseqs (0.7.0) should be installed within the qiime2 conda environment.
- Pandoc (2.5) should be located in your PATH.
- R (4.0.5) should be located in your PATH.
- R packages and versions: see session information at the end of each rmarkdown report.
All the code should be run from the project's root directory.
1.Clone or download this github repository to your local computer.
# clone the github repository
git clone https://github.com/yanxianl/Kizito_tilapia-perch-microbiota_2021.git
# delete the following folders
rm -rf \
data/intermediate/qiime2/compare_runs/ \
data/intermediate/qiime2/core_metrics_results*/ \
data/intermediate/qiime2/rpca*/ 2.Download raw sequence data, SILVA132 reference database and SILVA128 SEPP reference phylogeny (code/00_setup.ipynb).
# activate qiime2 environment
source $HOME/miniconda3/bin/activate
conda activate qiime2-2021.4
# launch jupyter notebook and run code/00_setup.ipynb interactively
jupyter notebook
# exit jupyter notebook after running the code by pressing Ctrl c in the terminal3.Sequence denoising (DADA2) and taxonomic assignment.
jupyter nbconvert --execute --to html code/01_qiime2_part1.ipynb4.Filter the feature tables to remove: 1).chloroplast/mitochondria sequences and those without a phylum-level taxonomic assignment; 2).low-prevalence features that only present in one sample; 3).contaminating features.
Rscript -e "rmarkdown::render('code/02_feature_filtering.Rmd')"5.Phylogeny and core-metrics-results.
jupyter nbconvert --execute --to html code/03_qiime2_part2.ipynb6.Import qiime2 artifacts into R.
Rscript -e "rmarkdown::render('code/04_qiime2R.Rmd')"7.Downstream data analysis to generate main results presented in the tilapia paper.
# taxonomic analysis
Rscript -e "rmarkdown::render('code/05_taxonomy_tilapia.Rmd')" &&
Rscript -e "rmarkdown::render('code/06_alpha_diversity_tilapia.Rmd')" &&
Rscript -e "rmarkdown::render('code/07_beta_diversity_tilapia.Rmd')" &&
Rscript -e "rmarkdown::render('code/08_differential_analysis_tilapia.Rmd')"8.Downstream data analysis to generate main results presented in the perch paper.
# taxonomic analysis
Rscript -e "rmarkdown::render('code/09_taxonomy_perch.Rmd')" &&
Rscript -e "rmarkdown::render('code/10_alpha_diversity_perch.Rmd')" &&
Rscript -e "rmarkdown::render('code/11_beta_diversity_perch.Rmd')" &&
Rscript -e "rmarkdown::render('code/12_differential_analysis_perch.Rmd')"- Add a driver script to automate all the analysis, e.g.,
make.