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

3.8.0

3.7.2

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-3.8.0.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-3.8.0-py3-none-any.whl (2.8 MB view details)

Uploaded Python 3

File details

Details for the file bohra-3.8.0.tar.gz.

File metadata

  • Download URL: bohra-3.8.0.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-3.8.0.tar.gz
Algorithm Hash digest
SHA256 aa6c19628620fe3c4912cbc6f6fe1b114e985a30bca5dd348528408953f92d0c
MD5 2c7b05ab18d4f3054df01dd6e3ee85e2
BLAKE2b-256 a16285ffb91d5e37ba1a3434fd10a420850c25f24e4dd47203784727d14b7bb8

See more details on using hashes here.

File details

Details for the file bohra-3.8.0-py3-none-any.whl.

File metadata

  • Download URL: bohra-3.8.0-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-3.8.0-py3-none-any.whl
Algorithm Hash digest
SHA256 bdc3c5077a501398e07441626404622e25bbffa6b772aa7ae116eefe6c9b3844
MD5 8e20e6d24e82dce62de2e0ecff64eeb0
BLAKE2b-256 dcad781c53a839ea2dba6899efb5d66caed64695d872692a90e2187398cd7f8d

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