crisprbuilder-tb 0.1.42

Collect and annotate Mycobacterium tuberculosis WGS data for CRISPR investigations.

CRISPRbuilder_TB

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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

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Collect and annotate Mycobacterium tuberculosis whole genome sequencing data for CRISPR investigation.

Requirements

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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

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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

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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

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First version of this package, which is 1.0.0 was published on August 2020.