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

3.7.1

3.7.0

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-3.7.1.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-3.7.1-py3-none-any.whl (2.8 MB view details)

Uploaded Python 3

File details

Details for the file bohra-3.7.1.tar.gz.

File metadata

  • Download URL: bohra-3.7.1.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-3.7.1.tar.gz
Algorithm Hash digest
SHA256 e2095900e7831ba6ae69054270d592d79a9a46e6bb5dcb1c70b4cd0f8d9089d7
MD5 0574d9f4e02dcd078253f1bad02e2430
BLAKE2b-256 92cc8c63dc1b0f2c4993f119fd6ad2c148e0b0f9f954cf67afd1b2e3082dcfdc

See more details on using hashes here.

File details

Details for the file bohra-3.7.1-py3-none-any.whl.

File metadata

  • Download URL: bohra-3.7.1-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-3.7.1-py3-none-any.whl
Algorithm Hash digest
SHA256 661b08878d5934351cad5b21206d247dd3dc2782e769f654ddae94ed5faa79b0
MD5 bf2ff3668d6561887d86a585eeb84142
BLAKE2b-256 24dbd2ddcf262a027a25c1889dc531a6482cf6093de9e9ad98d87083b4ed3975

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