crispr_finder

Code for paper "CRISPR spacer acquisition is a rare event in human gut microbiome"

Code for data summarization and visualization

• mathematical model: crispr_model.ipynb
• summarizing spacer rates in metagenomic data: crispr_MG_rate.ipynb
• summarizing spacer rates in WGS data: crispr_WGS_rate.ipynb
• summarizing HGT of spacers in B.longum species: crispr_HGT.ipynb

Code for sequencing data analysis - pipeline in crispr.py

• running cirsprcasefinder for WGS data: runCRISPRCasFinder.py
• merging and summarizzing crispr spacers + direct repeats: merge_spacer_filter.py
• detecting spacer acquisition in WGS data using maximum likelihood model: spacer_parsimony.py and spacer_parsimony_sum.py
• annotating spacers: annotate_spacer.py
• constructing the structure of CRISPR systems: spacer_structure.py
• extracting spacers + direct repeats from a specific species: DR_extract.py
• mapping direct repeats in metagenomes to WGS data: DR_MGmapping.py

Data

• containing data required to run jupyter notebooks