AutoBeditor

Project Introduction

AutoBeditor is an editing sequence design tool for CRISPR/Cas mediated base editing technology.

The main application scenarios of this software tool include:

1. sgRNA desgin

• Description：Support the design of high-throughput sgRNA for base editing.

2. Full process editing sequence design

• Description：Support the design of full process editing Sequence for base editing.

Installation

python packages

We suggest using Python 3.8 for AutoBeditor.

conda env create -f environment.yml

Usage & Example

1. sgRNA desgin

• Step 1: Upload the target information(TSV) file 、the genome(FAN) file、 the genome annotation(GFF) file to be edited.
• Step 2: provide the necessary configuration information.
  • Example configuration (json):

     param={ 
      "genome_release" : "GCF001",
      "host" : "yb01",
      "be_names" : ["Target-AID"],
      "pams" : ["NG"]
      } 

Execute:

python ./beditor/main.py 

Output:

• SgRNA Design Catalog(YB01)

These files will be generated in the XXX/AutoBeditor/data/output/ directory.

2. Full process editing sequence design

Input:

• Step 1: Upload the plasmid template(gb) file、the target information(TSV) file 、the genome(FAN) file、 the genome annotation(GFF) file、 the enzyme(CSV) file to be edited.
• Step 2: provide the necessary configuration information.
  • Example configuration (json):

     param={ 
      "genome_release" : "GCF001",
      "host" : "yb01",
      "be_names" : ["Target-AID"],
      "pams" : ["NG"]
      } 

Execute:

python main.py 

Output:

• SgRNA Design Catalog(YB01)
• result.xlsx

These files will be generated in the XXX/AutoBeditor/data/output/ directory.