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README.rst

1.. image:: https://github.com/marcelm/cutadapt/workflows/CI/badge.svg
2    :target: https://travis-ci.org/marcelm/cutadapt
3    :alt:
4
5.. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master
6    :target: https://pypi.python.org/pypi/cutadapt
7    :alt:
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9.. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg
10    :target: https://codecov.io/gh/marcelm/cutadapt
11    :alt:
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13.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
14    :target: http://bioconda.github.io/recipes/cutadapt/README.html
15    :alt: install with bioconda
16
17
18========
19Cutadapt
20========
21
22Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
23types of unwanted sequence from your high-throughput sequencing reads.
24
25Cleaning your data in this way is often required: Reads from small-RNA
26sequencing contain the 3’ sequencing adapter because the read is longer than
27the molecule that is sequenced. Amplicon reads start with a primer sequence.
28Poly-A tails are useful for pulling out RNA from your sample, but often you
29don’t want them to be in your reads.
30
31Cutadapt helps with these trimming tasks by finding the adapter or primer
32sequences in an error-tolerant way. It can also modify and filter single-end
33and paired-end reads in various ways. Adapter sequences can contain IUPAC
34wildcard characters. Cutadapt can also demultiplex your reads.
35
36Cutadapt is available under the terms of the MIT license.
37
38Cutadapt development was started at `TU Dortmund University <https://www.tu-dortmund.de>`_
39in the group of `Prof. Dr. Sven Rahmann <https://www.rahmannlab.de/>`_.
40It is currently being developed within
41`NBIS (National Bioinformatics Infrastructure Sweden) <https://nbis.se/>`_.
42
43If you use Cutadapt, please cite
44`DOI:10.14806/ej.17.1.200 <http://dx.doi.org/10.14806/ej.17.1.200>`_ .
45
46
47Links
48-----
49
50* `Documentation <https://cutadapt.readthedocs.io/>`_
51* `Source code <https://github.com/marcelm/cutadapt/>`_
52* `Report an issue <https://github.com/marcelm/cutadapt/issues>`_
53* `Project page on PyPI (Python package index) <https://pypi.python.org/pypi/cutadapt/>`_
54* `Follow @marcelm_ on Twitter <https://twitter.com/marcelm_>`_
55* `Wrapper for the Galaxy platform <https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt>`_
56