Scripts and misc. for the paper:

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes from natural populations

This project was funded by the Univeristy of California, Irvine Malaria Inititive

NOTE: Large datafiles (eg. vcf files) will gladly be provided upon request.

• sample_meta.xlsx : sample lists and metadata for the VGL (Vector Genetics Lab) samples used in this study
• notes.md : working notes for running chopchop on all transcripts from a genome
• all_transcript_runs/ : scripts and log files from running chopchop on all transcripts for AgamP4.11 and AaegL5.1
• utils/ : additional small scripts used in preparing datafiles for chopchop
• parsing/ : iPython notebooks used to process all_transcript_runs results
• variants/ : iPython notebooks used to process variant data, collate it with all_transcript_runs, and produce statistics and figures