'Sequana': a Set of Snakemake NGS pipelines

'Sequana': a Set of Snakemake NGS pipelines - Published in JOSS (2017)
https://github.com/sequana/sequana

Keywords

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

Keywords from Contributors

bioinformatics singularity sniffer sequence sam2bam phylogeny genbank2fasta genbank2embl fasta2fastq embl2genbank

Last synced: 2 months ago
JSON representation

Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

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 (almost 10 years ago)
Default Branch: main
Last Pushed: 2025-10-16T08:51:50.000Z (2 months ago)
Last Synced: 2025-10-25T02:48:35.184Z (2 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
Releases: 0
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 ynced at: 2023-03-06T02:06:16.887Z
Profile URL: https://github.com/sequana

GitHub Events

Total

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

Last Year

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

Committers metadata

Last synced: 2 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

Committer domains:

Issue and Pull Request metadata

Last synced: 2 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)

Package metadata

Total packages: 1
Total downloads:
- pypi: 864 last-month
Total dependent packages: 12
Total dependent repositories: 14
Total versions: 106
Total maintainers: 1

pypi.org: sequana

A set of standalone application and pipelines dedicated to NGS analysis

Homepage: https://sequana.readthedocs.io
Documentation: https://sequana.readthedocs.io
Licenses: BSD 3-Clause License Copyright (c) 2016-2021, Sequana Development Team (https://sequana.readthedocs.io) All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Sequana nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Latest release: 0.19.3 (published 2 months ago)
Last Synced: 2025-10-18T12:08:03.597Z (2 months ago)
Versions: 106
Dependent Packages: 12
Dependent Repositories: 14
Downloads: 864 Last month
Rankings:
- Dependent packages count: 1.251%
- Dependent repos count: 3.862%
- Average: 5.055%
- Stargazers count: 6.206%
- Downloads: 6.481%
- Forks count: 7.476%
Maintainers (1)
- cokelaer

Score: 14.1383546373841

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