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

3.7.1

This version

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-3.7.0.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-3.7.0-py3-none-any.whl (2.8 MB view details)

Uploaded Python 3

File details

Details for the file bohra-3.7.0.tar.gz.

File metadata

  • Download URL: bohra-3.7.0.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-3.7.0.tar.gz
Algorithm Hash digest
SHA256 e31a44d5219fb7385079267f6e2673d5e84a254212c7b8d921752ad6ce2e63c6
MD5 e878dc7bd496a333325e3702aa3b28c9
BLAKE2b-256 9ef9f5968dfb8bbe43c52a72a97ecd2d9b1282e8bd39f16852a80c6f90115d67

See more details on using hashes here.

File details

Details for the file bohra-3.7.0-py3-none-any.whl.

File metadata

  • Download URL: bohra-3.7.0-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-3.7.0-py3-none-any.whl
Algorithm Hash digest
SHA256 4268dfdf1ed21b757de52cecdcf29e204407ad019cf7550e38cde9f0559e5702
MD5 634e2085f44ccafbd46902e43857a3bf
BLAKE2b-256 492547e139c84b5612892a4480c157304cc8a5ab7da47e1d7a23bf287b1ad73b

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