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

Navigation

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
Report project as malware

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

Release history Release notifications | RSS feed

This version

3.6.7

3.6.6

3.6.5

3.6.4

3.6.3

3.6.2 yanked

Reason this release was yanked:

mistaken push

3.6.1

3.6.0

3.5.2

3.5.1

3.5.0

3.4.3

3.4.2

3.4.1

3.4.0

3.3.0

3.2.11

3.2.9

3.2.5

3.2.4

3.2.0

3.0.6

3.0.3

3.0.2

3.0.1

3.0.0

2.3.10

2.3.9

2.3.8

2.3.7

2.3.6

2.3.5

2.3.4

2.3.3

2.3.2

2.3.1

2.3.0

2.2.1

2.2.0

1.2.20

1.2.19

1.2.18

1.2.16

1.2.15

1.2.14

1.2.13

1.2.12

1.2.11

1.2.10

1.2.9

1.2.8

1.2.7

1.2.6

1.2.5

1.2.4

1.2.3

1.2.2

1.2.1

1.2.0

1.1.8

1.1.7

1.1.6

1.1.5

1.1.4

1.1.3

1.1.2

1.1.1

1.1.0

1.0.27

1.0.26

1.0.25

1.0.24

1.0.23

1.0.22

1.0.20

1.0.19

1.0.18

1.0.17

1.0.16

1.0.15

1.0.13

1.0.12

1.0.11

1.0.10

1.0.9

1.0.7

1.0.6

1.0.5

1.0.4

1.0.3

1.0.1

Download files

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

Source Distribution

bohra-3.6.7.tar.gz (2.6 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

bohra-3.6.7-py3-none-any.whl (2.8 MB view details)

Uploaded Python 3

File details

Details for the file bohra-3.6.7.tar.gz.

File metadata

  • Download URL: bohra-3.6.7.tar.gz
  • Upload date:
  • Size: 2.6 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.13.2

File hashes

Hashes for bohra-3.6.7.tar.gz
Algorithm Hash digest
SHA256 a9a0c3f1fb46ff49ee611adbb453bfb40d388c2efdd79e94eb8def3ae8827991
MD5 c0e29ae005bf6bd2e295d0ebdc98ab24
BLAKE2b-256 82210a99ec2200051a2427392f7aaf9c25e95fc0507f9deb83ac29366d43b021

See more details on using hashes here.

File details

Details for the file bohra-3.6.7-py3-none-any.whl.

File metadata

  • Download URL: bohra-3.6.7-py3-none-any.whl
  • Upload date:
  • Size: 2.8 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.13.2

File hashes

Hashes for bohra-3.6.7-py3-none-any.whl
Algorithm Hash digest
SHA256 ba5db9b3378c0f7b61b292461367ab1ad42bdceec53b344c56903ba2de27cd1c
MD5 72e79b0aba15a42a845d03cc7e7a93e9
BLAKE2b-256 f498d4d88393d050cb03464ff0940cc54be9027f89325d1e129fec2163721156

See more details on using hashes here.

Supported by

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