cutadapt
Cutadapt removes adapter sequences from sequencing reads
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 32 committers (9.4%) from academic institutions -
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary
Keywords
bioinformatics
python
Keywords from Contributors
closember
Last synced: 6 months ago
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JSON representation
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Repository
Cutadapt removes adapter sequences from sequencing reads
Basic Info
- Host: GitHub
- Owner: marcelm
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://cutadapt.readthedocs.io
- Size: 3.91 MB
Statistics
- Stars: 559
- Watchers: 23
- Forks: 134
- Open Issues: 95
- Releases: 3
Topics
bioinformatics
python
Created over 13 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Contributing
License
Citation
README.rst
.. image:: https://github.com/marcelm/cutadapt/workflows/CI/badge.svg
:alt:
.. image:: https://img.shields.io/pypi/v/cutadapt.svg
:target: https://pypi.python.org/pypi/cutadapt
:alt:
.. image:: https://codecov.io/gh/marcelm/cutadapt/branch/main/graph/badge.svg
:target: https://codecov.io/gh/marcelm/cutadapt
:alt:
.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
:target: http://bioconda.github.io/recipes/cutadapt/README.html
:alt: install with bioconda
========
Cutadapt
========
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
types of unwanted sequence from your high-throughput sequencing reads.
Cleaning your data in this way is often required: Reads from small-RNA
sequencing contain the 3’ sequencing adapter because the read is longer than
the molecule that is sequenced. Amplicon reads start with a primer sequence.
Poly-A tails are useful for pulling out RNA from your sample, but often you
don’t want them to be in your reads.
Cutadapt helps with these trimming tasks by finding the adapter or primer
sequences in an error-tolerant way. It can also modify and filter single-end
and paired-end reads in various ways. Adapter sequences can contain IUPAC
wildcard characters. Cutadapt can also demultiplex your reads.
Cutadapt is available under the terms of the MIT license.
Cutadapt development was started at `TU Dortmund University `_
in the group of `Prof. Dr. Sven Rahmann `_ .
Links
-----
* `Documentation `_
* `Project page on PyPI (Python package index) `_
Owner
- Name: Marcel Martin
- Login: marcelm
- Kind: user
- Location: Stockholm
- Repositories: 9
- Profile: https://github.com/marcelm
Citation (CITATION.cff)
cff-version: 1.2.0
title: Cutadapt
message: "If you use this software, please cite DOI 10.14806/ej.17.1.200 as below"
authors:
- given-names: Marcel
family-names: Martin
orcid: 'https://orcid.org/0000-0002-0680-200X'
url: 'https://cutadapt.readthedocs.io/'
repository-code: 'https://github.com/marcelm/cutadapt/'
license: MIT
preferred-citation:
type: article
authors:
- given-names: Marcel
family-names: Martin
orcid: 'https://orcid.org/0000-0002-0680-200X'
doi: 10.14806/ej.17.1.200
journal: EMBnet.journal
month: 5
year: 2011
start: 10
end: 12
title: 'Cutadapt removes adapter sequences from high-throughput sequencing reads'
volume: 17
issue: 1
GitHub Events
Total
- Issues event: 58
- Watch event: 41
- Delete event: 23
- Issue comment event: 103
- Push event: 28
- Pull request event: 12
- Fork event: 6
- Create event: 19
Last Year
- Issues event: 58
- Watch event: 41
- Delete event: 23
- Issue comment event: 103
- Push event: 28
- Pull request event: 12
- Fork event: 6
- Create event: 19
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Marcel Martin | m****n@s****e | 2,160 |
| Ruben Vorderman | r****n@l****l | 117 |
| John Didion | g****b@d****t | 7 |
| Kyle Beauchamp | k****b@c****m | 6 |
| Chris Mitchell | c****7@g****m | 5 |
| Tim Booth | t****h@e****k | 4 |
| James Casbon | j****n@p****m | 3 |
| Peter Cock | p****k@g****m | 3 |
| Marcel Martin | m****r@f****e | 2 |
| Space Robot | 2 | |
| Lance Parsons | l****s@p****u | 2 |
| Frédéric Mahé | x****b@x****g | 2 |
| Vittorio Zamboni | z****i@a****g | 1 |
| Adel Qalieh | a****q | 1 |
| Anicet Ebou | a****u@g****m | 1 |
| Dave Lawrence | d****w@g****m | 1 |
| Don Kirkby | d****y | 1 |
| Greg Knaddison | g****n@g****m | 1 |
| Jan van Haarst | j****n@v****t | 1 |
| wlokhorst | w****t@h****m | 1 |
| Wolfgang Gerlach | w****h@m****v | 1 |
| Tyghe Vallard | v****t@g****m | 1 |
| Sylvain | s****b@g****m | 1 |
| Stephen Kazakoff | s****f@g****m | 1 |
| Owen Solberg | o****n | 1 |
| Michael Kluge | k****m | 1 |
| Merve B. Duman | 9****n | 1 |
| Matt Shirley | m****5@g****m | 1 |
| Mathias Walter | m****s@w****d | 1 |
| Luchao Qi | 4****i | 1 |
| and 2 more... | ||
Committer Domains (Top 20 + Academic)
walter.gd: 1
mcs.anl.gov: 1
vanhaarst.net: 1
appliedgenomics.org: 1
xn--mah-dma.org: 1
princeton.edu: 1
freenet.de: 1
popgentech.com: 1
ed.ac.uk: 1
counsyl.com: 1
didion.net: 1
lumc.nl: 1
scilifelab.se: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 182
- Total pull requests: 32
- Average time to close issues: 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 133
- Total pull request authors: 8
- Average comments per issue: 3.36
- Average comments per pull request: 2.56
- Merged pull requests: 23
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 40
- Pull requests: 5
- Average time to close issues: 15 days
- Average time to close pull requests: 8 days
- Issue authors: 37
- Pull request authors: 4
- Average comments per issue: 1.3
- Average comments per pull request: 1.8
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- marcelm (13)
- rhpvorderman (11)
- y9c (6)
- racng (4)
- luigallucci (3)
- marwa38 (3)
- peterjc (2)
- fjossandon (2)
- junjunlab (2)
- cpavloud (2)
- nr0cinu (2)
- sayeraselvan (2)
- ramongallego (2)
- Flower9618 (2)
- yfarjoun (2)
Pull Request Authors
- rhpvorderman (19)
- marcelm (11)
- y9c (6)
- mervebduman (2)
- odoublewen (2)
- MaWeffm (2)
- RPINerd (2)
- geertvandeweyer (1)
Top Labels
Issue Labels
API (3)
feature-request (2)
question (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 30,311 last-month
- Total docker downloads: 132,567
- Total dependent packages: 20
- Total dependent repositories: 88
- Total versions: 69
- Total maintainers: 1
pypi.org: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
- Homepage: https://cutadapt.readthedocs.io/
- Documentation: https://cutadapt.readthedocs.io/
- License: mit
-
Latest release: 1.9.1
published about 10 years ago
Rankings
Docker downloads count: 0.8%
Dependent packages count: 0.9%
Average: 1.3%
Dependent repos count: 1.6%
Downloads: 1.9%
Maintainers (1)
Last synced:
6 months ago
Dependencies
pyproject.toml
pypi
- dnaio >= 0.9.1
- xopen >= 1.6.0
.github/workflows/ci.yml
actions
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.github/workflows/pyinstaller.yml
actions
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doc/requirements.txt
pypi
- sphinx_better_subsection *
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setup.py
pypi