Metadata-Version: 2.4
Name: bohra
Version: 3.0.0
Summary: A bioinformatics pipeline for analysing short read Illumina data microbiological public health.
Project-URL: Homepage, https://github.com/kristyhoran/bohra
Author-email: Kristy Horan <kristyhoran15@gmail.com>
License-Expression: GPL-3.0-or-later
License-File: LICENSE.txt
Keywords: bioinformatics,microbiology,public health
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.11
Requires-Dist: altair
Requires-Dist: biopython==1.85
Requires-Dist: click
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: psutil
Requires-Dist: pytest
Requires-Dist: scikit-learn==1.7.1
Requires-Dist: scipy==1.16.1
Provides-Extra: tests
Requires-Dist: flake8; extra == 'tests'
Requires-Dist: pandas; extra == 'tests'
Requires-Dist: pytest; extra == 'tests'
Description-Content-Type: text/markdown

[![Python 3.9](https://img.shields.io/badge/python-3.9-blue.svg)](https://www.python.org/downloads/release/python-390/)
[![GitHub release (latest by date)](https://img.shields.io/github/v/release/MDU-PHL/bohra)](https://github.com/MDU-PHL/bohra/releases/latest)
[![Conda Downloads](https://img.shields.io/conda/dn/bioconda/bohra)](https://anaconda.org/bioconda/bohra)
[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

**Bohra is currently undergoing some significant upgrades and redevelopment. We appreciate your patience while we make these changes. For those interested you can find some preliminary installation and usage instructions [here](https://mdu-phl.github.io/bohra/). The current stable version detailed below is still ofcourse available.**

# Bohra

Bohra is microbial genomics pipeline, designed predominantly for use in public health, but may also be useful in research settings. At a minimum the pipeline takes as input a tab-delimited file with the isolate IDs followed by the path to READ1 and READ2, where reads are illumina reads (other platforms are not supported at this stage).

For detailed usage information please see our [wiki](https://github.com/MDU-PHL/bohra/wiki)

## Recent changes to bohra
* Install script to setup dependencies for you.
* babykraken download as part of the dependency installation.
* Addition of typers
    * [Kleborate](https://github.com/klebgenomics/Kleborate/wiki)
    * [stype](https://github.com/MDU-PHL/salmonella_typing) (NATA accredited ISO15189)
    * [meningotype](https://github.com/MDU-PHL/meningotype) (NATA accredited ISO15189)
    * [lissero](https://github.com/MDU-PHL/lissero) (NATA accredited ISO15189)
    * [ngmaster](https://github.com/MDU-PHL/ngmaster)
    * [ectyper](https://github.com/phac-nml/ecoli_serotyping)

**Comming soon**

* Improved report structure
* Mtb AMR


**Accreditation**

Many of the underlying tools of the bohra pipeline are NATA accredited by [MDU](https://biomedicalsciences.unimelb.edu.au/departments/microbiology-Immunology/research/services/) Victoria Australia (ISO1589).

* `snippy` and `snippy-core` version 4.4.5  
* `abritamr` 
* `stype`
* `meningotype`
* `lissero`

### Motivation

Bohra was inspired by Nullarbor (https://github.com/tseemann/nullarbor) to be used in public health microbiology labs for analysis of short reads from microbiological samples. The pipeline is written in [Nextflow](https://www.nextflow.io).

### Etymology

Bohra the name of an exinct species of tree kangaroo that lived on the Nullarbor plain in Australia. The name was chosen to reflect the fact that it will be predominantly used to build *trees*, relies on [*snippy*](https://github.com/tseemann/snippy) (named for a very famous kangaroo) and was inspired by [*nullarbor*](https://github.com/tseemann/nullarbor). 


