https://github.com/marcelm/cutadapt

Cutadapt removes adapter sequences from sequencing reads
https://github.com/marcelm/cutadapt

bioinformatics python

Last synced: 8 days ago
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Cutadapt removes adapter sequences from sequencing reads

• Host: GitHub
• URL: https://github.com/marcelm/cutadapt
• Owner: marcelm
• License: mit
• Created: 2012-06-06T20:26:25.000Z (almost 13 years ago)
• Default Branch: main
• Last Pushed: 2025-04-03T07:44:35.000Z (19 days ago)
• Last Synced: 2025-04-12T18:35:24.422Z (9 days ago)
• Topics: bioinformatics, python
• Language: Python
• Homepage: https://cutadapt.readthedocs.io
• Size: 3.77 MB
• Stars: 544
• Watchers: 23
• Forks: 134
• Open Issues: 81
• Metadata Files:
  • Readme: README.rst
  • Changelog: CHANGES.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Citation: CITATION.cff

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README

        
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========

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 `_.

It is currently being developed within

`NBIS (National Bioinformatics Infrastructure Sweden) `_.

Citation

--------

If you use Cutadapt, please cite

`DOI:10.14806/ej.17.1.200 `_ .

Links

-----

* `Documentation `_

* `Source code `_

* `Report an issue `_

* `Project page on PyPI (Python package index) `_

* `Wrapper for the Galaxy platform `_