EXCAVATE-HT Documentation

EXCAVATE-HT (EXtraction of Common Allelic VAriants for Targeted Editing in High-Throughput) is a Python-based bioinformatic pipeline to mine population and personalised variant data to identify genomic loci targetable for CRISPR-based allele-specific editing and create single and dual-gRNA libraries to enable high-throughput screens of these edits.

Contents

• Introduction
• Installation
  • Prerequisites
  • Set Up
  • Prepare input data files
  • Using EXCAVATE-HT
  • Off-target Analysis Setup
  • Troubleshooting
• Parameters
• EXCAVATE-HT Modes
  • excavate-ht generate
  • excavate-ht pair
• EXCAVATE-HT Examples
  • Example run: Generating a paired dual-gRNA library
  • Example run: Generating a single-gRNA library, editing it, then pairing to create a dual-gRNA library
• API Reference
  • add_common_args()
  • add_generate_parser()
  • add_pair_parser()
  • apply_pairing()
  • initialize_cas_obj()
  • load_variant_data()
  • main()
  • run_generate()
  • run_off_targets()
  • run_pairing()
  • Cas
  • SaCas9
  • all_guides_var_info()
  • cas_obj
  • count_exact_matches()
  • create_custom_cas_obj()
  • create_exclusion_pos_set()
  • create_gens()
  • create_regex_pam()
  • find_guides()
  • fixed_point_pair()
  • getaltseq()
  • init_worker()
  • makeseq()
  • one_mismatch()
  • output_bed_format()
  • random_pair()
  • search_pattern()
  • split_phased()
  • targetable_vars()
  • tiling_pair()
• Contributing
  • Reporting Issues

Indices and tables

• Index

• Module Index

• Search Page