CRISPRbuilder_TB
This README.md gives you the gist of the CRISPRbuilder_TB package. Please refer to crisprbuilder_tb.ipynb included in the package and readable on GitHub for more detailed explanation.
Purpose of this package
Collect and annotate Mycobacterium tuberculosis whole genome sequencing data for CRISPR investigation.
Requirements
CRISPRbuilder_TB needs the following dependencies to work:
- python >= "3.6"
- xlrd >= "1.2.0"
- xmltodict >= "0.12.0"
- biopython >= "1.77"
- parallel-fastq-dump >= "0.6.5"
- blast >= "2.10.1"
- blastn >= "2.7.1"
These different versions are automatically downloaded when installing the CRISPRbuilder_TB package.
Installation
Make sure you're using a version of Python higher or equal to 3.6. Install the package by writing in the command prompt:
pip install crisprbuilder_tb.
How to use this package
The most often common instruction for this package is:
python -m crisprbuilder_tb --collect {SRA_reference}.
See the documentation criprbuilder-tb.ipynb for a comprehensive explanation.
History
First version of this package, which is 1.0.0 was published on August 2020.