SNP23: Analyzing the genomic differences between wild type strains (as published in reference genomes) and strains kept under lab conditions (resequenced by the Segrè lab in 2019)
- What are the SNPs in the re-sequenced genomes (vs original genomes? I.e., how many SNAPs/genome, location of SNPs, what genes are affected?
- What are other genomic changes compared with the original genome? E.g, rearrangements, paralogs.
- Is there conservancy in the number of SNPs based on phylogenetic relationships? I.e Do closely-related microbes undergo similar changes?
Shared Notes on Google Drive: https://drive.google.com/drive/folders/1ZNowof5NB3n_OAjHu4QRoAtlrP9T6WHK?usp=drive_link
Breseq is insalled on the BU SCC, along with all of the dependencies to run this pipeline. To activate the conda environment with these tools, run:
module load miniconda
conda activate /projectnb/hfsp/SNP23/envs/brese