A bioinformatics pipeline for analysing short read Illumina data microbiological public health.

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  • License Expression: GPL-3.0-or-later
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  • Author: Kristy Horan
  • Tags bioinformatics , microbiology , public health
  • Requires: Python >=3.11
  • Provides-Extra: tests
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Project description

CI GitHub release (latest by date) Conda Downloads Python License: GPL v3

Bohra

Bohra Logo

Bohra is an extensive pipeline for taking genome sequences (short reads or assemblies) and running common bioinformatics assays across the, including genotyping, AMR detection, and phylogenetics.

Bohra is a modern replacement for the Nullarbor pipeline. It is written in Python and Nextflow instead of Perl and Make.

Installation

  1. Install the base packaghe
% conda create -n bohra -c bioconda bohra
% borha --version
  1. Install all the analysis modules. This can take a long time (10-60 min) but it's worth it!
% bohra deps install
  1. Test everthing worked ok
% bohra test --cpus 8

Documentation

Read the Bohra website to learn how to use all the availaile features.

Workflow

Bohra workflow

Authors

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for kristyhoran from gravatar.com kristyhoran

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License Expression: GPL-3.0-or-later
    SPDX License Expression
  • Author: Kristy Horan
  • Tags bioinformatics , microbiology , public health
  • Requires: Python >=3.11
  • Provides-Extra: tests
Classifiers

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