Code and data for the Kalan lab study:
Large-scale investigation for antimicrobial activity reveals novel defensive
species across the healthy skin microbiome.
Nguyen UT, Salamzade R, Sandstrom S, Swaney MH, Townsend EC, Wu SY, Cheong JZA,
Sardina JA, Ludwikoski I, Rybolt M, Wan H, Carlson CM, Ferro J, McArthur O,
Suh WS, Zarnowski R, Andes DR, Currie CR, Kalan LR
Most relevant files can be found under: Figures/Final. Each folder, corresponding to a Figure or Extended Data Figure, has a README.md describing the contents. While AI was not used for the analyses themselves, we did use AI to draft these README files which we then manually edited as necessary. The term "LK" appears in some files and is an alias used to describe isolates/genomes in EPIC.
Key software (and their versions) used for analyses include:
- fastp (v0.20.0)
- unicycler (v0.4.7)
- dRep (v3.2.2)
- GTDB-Tk (v1.7.0) with GTDB release 202
- FastANI (v1.32)
- GToTree (v1.6.36)
- PareTree (v1.0.2)
- The iTol web application
- antiSMASH (v6.0.0)
- BiG-SCAPE (v1.1.5)
- zol (v1.3.11)
- BiG-MAP (downloaded March 22, 2023 from GitHub)
- BiG-SLICE (v1.1.1)
- GECCO (v0.9.6)
- PyHMMER (v0.11.0)
- RGI (v6.0.1)
- Branchwater (accessed in October 2023).