JOSS: https://github.com/sequana/sequana/

coverage de-novo ngs pacbio rna-seq sequanix snakemake taxonomy variant-calling

Score: 7.346010209913293

Last synced: about 3 hours ago
JSON representation

Repository metadata:

Sequana: a set of Snakemake NGS pipelines

Host: GitHub
URL: https://github.com/sequana/sequana/
Owner: sequana
License: bsd-3-clause
Created: 2016-03-07T14:00:07.000Z (over 10 years ago)
Default Branch: main
Last Pushed: 2025-10-16T08:51:50.000Z (8 months ago)
Last Synced: 2025-10-25T02:48:35.184Z (8 months ago)
Topics: coverage, de-novo, ngs, pacbio, rna-seq, sequanix, snakemake, taxonomy, variant-calling
Language: Jupyter Notebook
Homepage: http://sequana.readthedocs.io
Size: 35.7 MB
Stars: 148
Watchers: 5
Forks: 28
Open Issues: 7
Metadata Files:
- Readme: README.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE

Owner metadata:

Name: sequana
Login: sequana
Email:
Kind: organization
Description:
Website:
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/17704295?v=4
Repositories: 17
Last Synced at: 2023-03-06T02:06:16.887Z
Profile URL: https://github.com/sequana

GitHub Events

Total

Create event: 4
Fork event: 1
Gollum event: 5
Issue comment event: 7
Issues event: 8
Pull request event: 10
Push event: 10
Release event: 5
Watch event: 7
Total: 57

Last Year

Create event: 3
Fork event: 1
Gollum event: 5
Issue comment event: 4
Issues event: 4
Pull request event: 8
Push event: 8
Release event: 4
Watch event: 5
Total: 42

Committers metadata

Last synced: 8 months ago

Total Commits: 5,816
Total Committers: 10
Avg Commits per committer: 581.6
Development Distribution Score (DDS): 0.262

Commits in past year: 63
Committers in past year: 2
Avg Commits per committer in past year: 31.5
Development Distribution Score (DDS) in past year: 0.016

Name	Email	Commits
Thomas Cokelaer	c**r@g**m	4293
Dimitri Desvillechabrol	d**l@g**m	679
rlegendre	r**r@p**r	372
rlegendre	r**e@p**r	306
Etienne Kornobis	e**s@g**m	125
mcardon	m**n@p**r	30
Maelle	m**e@g**m	5
Arfon Smith	a****n	3
Quentin LETOURNEUR	q**r@p**r	2
Rachel LEGENDRE	r**r@t**r	1

Issue and Pull Request metadata

Last synced: 8 months ago

Total issues: 54
Total pull requests: 139
Average time to close issues: 8 months
Average time to close pull requests: 2 days
Total issue authors: 8
Total pull request authors: 3
Average comments per issue: 0.5
Average comments per pull request: 0.76
Merged pull request: 129
Bot issues: 0
Bot pull requests: 0

Past year issues: 5
Past year pull requests: 9
Past year average time to close issues: about 1 month
Past year average time to close pull requests: 1 day
Past year issue authors: 2
Past year pull request authors: 2
Past year average comments per issue: 0.6
Past year average comments per pull request: 0.56
Past year merged pull request: 7
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/sequana/sequana/

Top Issue Authors

cokelaer (44)
khourhin (3)
ddesvillechabrol (2)
Lutri22 (1)
vladsavelyev (1)
Saurias92 (1)
Caizhengwen123 (1)
mptrsen (1)

Top Pull Request Authors

cokelaer (111)
khourhin (21)
ddesvillechabrol (7)

Top Issue Labels

enhancement (8)
bug (8)
refactoring (3)
New features/enhancement (3)
3 (2)
1 (2)
documentation (2)
Todo (2)
5 (1)
question (1)

Top Pull Request Labels

enhancement (2)

Dependencies

doc/requirements.txt pypi

sequana_sphinxext *
sphinx >=3
sphinx_rtd_theme *

requirements.txt pypi

UpSetPlot *
adjusttext *
bioservices >=1.10.0
brokenaxes *
bx-python *
click >=8.1.0
colorlog >=3.1.0
colormap *
cookiecutter *
cython *
docutils *
easydev >=0.11.1
gseapy *
itolapi *
lxml *
matplotlib *
matplotlib-venn *
mock *
multiqc <=1.11
packaging *
pandas >=0.22
plotly *
psutil *
pykwalify *
pysam >=0.16
ruamel.yaml >=0.16.0
scikit-learn *
scipy *
seaborn *
snakemake >=7.3.1
statsmodels *
tqdm *
vcfpy *
xlrd *

requirements_pipelines.txt pypi

sequana_coverage *
sequana_demultiplex *
sequana_denovo *
sequana_fastqc *
sequana_mapper *
sequana_quality_control *
sequana_rnaseq *
sequana_variant_calling *

.github/workflows/main.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/pypi.yml actions

actions/checkout main composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish release/v1 composite

docker/sequana/Dockerfile docker

sequana/sequana_conda_ngs latest build

docker/sequana_conda_core/Dockerfile docker

sequana/sequana_core latest build

docker/sequana_conda_ngs/Dockerfile docker

sequana/sequana_conda_core latest build

docker/sequana_core/Dockerfile docker

ubuntu 16.04 build

docker/sequana_coverage/Dockerfile docker

sequana/sequana latest build

docker/sequana_taxonomy/Dockerfile docker

sequana/sequana latest build

environment.yml pypi

setup.py pypi

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