Despres_et_al_2024

Jupyter notebooks used for data analysis and figure generation of Despres et al 2024. Raw sequence files can be downloaded from the NCBI SRA https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1061126, and other files required are included in the sub repositories.

Software used:

• FastQC v0.11.5
• Trimmomatic v0.39
• PANDAseq 2.11
• vsearch v2.7.1
• Python 3.7.9

Python package versions:

• pandas 1.2.1
• numpy 1.19.2
• matplotlib 3.3.2
• scipy 1.5.2
• biopython 1.78
• seaborn 0.11.1

DMS_validation

Contains files and code used to perform DMS library QC. Generates initial abundance values for the DMS 5-FC selection assay.

5FC_selection

Contains files and code used to identify LOF alleles from the DMS assay.

• DMS_analysis_5FC.ipynb: Goes from raw sequencing data to variant abundance.
• variant_abundance.ipynb: Computes DMS scores and generates figures S2, S3, S4, S5

single_colony_genotyping

Contains files and code used to analyze the single colony sequencing data.

• single_colony_genotyping.ipynb generates figures 2a-c S6, S7, S8, S9

haploid_validations.ipynb

Analyze growth curve data for haploid parental strains used in the validation assays. Generates figure S10.

validations_analysis

Contains files and code used to analyze the validation assays.

• validations_analysis.ipynb generates figures 3, S11, S12, S14, S15b-d

haploid_validations.ipynb

Analyze haploinsufficiency dose-response growth curve data and generate figure S13.

DHFR_PCA_data.ipynb

Analyze DHFR-PCA growth curve data and generate figure S16bc

activity_stability

Contains files and code used to analyze enzymatic and stability assays.

• activity_stability.ipynb generates figures 4ab

misc data

Contains raw growth curve data for the haploid validations, the haploinsufficiency test, and the DHFR-PCA assay.