SmellyShirts
Scripts and data to reproduce results for the paper:
The T-shirt microbiome is distinct between individuals and shaped by washing and fabric type (Sterndorff and Russel et al., Environmental Research, 2020): https://www.sciencedirect.com/science/article/abs/pii/S001393512030342X
How to reproduce results
A phyloseq object with all the prepared data can be found in data/physeq.RData
Preparation
- Get sequences from http://www.ncbi.nlm.nih.gov/bioproject/594290
- Run data/Cutadapt_seq.txt to remove primers from sequences
- Get reference databases from doi:10.5281/zenodo.801827
- Run data/Cutadapt_ref.txt to remove primers and everything outside V3V4 region from sequences
R analysis
- Run data/load_data.R script (R 3.4.3)
- Run the remaning .R scripts (R 3.5.2)
Software
- Cutadapt 1.14 (doi:10.14806/ej.17.1.200)
- mafft v7.376 (doi:10.1093/molbev/mst010)
- FastTree 2.1.10 (doi:10.1371/journal.pone.0009490)
- GNU parallel (O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine)
- Bowtie v2.2.3 (doi:10.1038/nmeth.1923)
- Samtools v1.5 (doi:10.1093/bioinformatics/btp352)
- Gephi 0.9.2
- R 3.4.3 (no link means they are from CRAN)
- dada2 1.7.7 (doi:10.1038/nmeth.3869)
- phyloseq 1.22.3 (doi:10.1371/journal.pone.0061217)
- foreach 1.4.4
- ips 0.0-7
- ape 5.0
- R 3.5.2 (no link means they are from CRAN)
- DAtest 2.7.15 (doi:10.1101/241802)
- ggplot2 3.1.0
- vegan 2.5-4
- nlme 3.1-137
- multcomp 1.4-1
- foreach 1.4.4
- phyloseq 1.26.1
- COEF 0.0.0.9 (https://github.com/Russel88/COEF)
- eulerr 5.1.0
Databases
- Taxonomy: RDP 16 release 11.5 train set and species set (doi:10.1093/nar/gkt1244, doi:10.5281/zenodo.801828)
- 16S rRNA gene copy numbers: rrnDB-5.4 RDP (doi:10.1093/nar/gku1201)