Skip to main content

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

Project description

CircleCI Python 3.9


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

Recent changes to bohra

  • Install script to setup dependencies for you.
  • babykraken download as part of the dependency installation.
  • Addition of typers

Comming soon

  • Improved report structure
  • Mtb AMR


Many of the underlying tools of the bohra pipeline are NATA accredited by MDU Victoria Australia (ISO1589).

  • snippy and snippy-core version 4.4.5
  • abritamr
  • stype
  • meningotype
  • lissero


Bohra was inspired by Nullarbor ( to be used in public health microbiology labs for analysis of short reads from microbiological samples. The pipeline is written in Nextflow.


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 (named for a very famous kangaroo) and was inspired by nullarbor.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bohra-2.3.2.tar.gz (2.0 MB view hashes)

Uploaded source

Built Distribution

bohra-2.3.2-py3-none-any.whl (2.1 MB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page