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Repository cutadapt
Name: cutadapt
Owner: lparsons
Synopsis: Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

http://dx.doi.org/10.14806/ej.17.1.200
Content homepage: https://cutadapt.readthedocs.org/en/stable/
Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/2d6671b10919
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt
Type: unrestricted
Revision: 8:2d6671b10919
This revision can be installed: True
Times cloned / installed: 13549

Repository README files - may contain important installation or license information

Readme files
Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/) Installation - Tool Shed --------------------------- The recommended way to install cutadapt as a tool in Galaxy is to the use the Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed). This will allow cutadapt to be installed automatically and keep track of older versions of cutadapt and the tool wrapper. Installation - Manual --------------------- 1 - Install the cutadapt package and make sure it is in path for Galaxy 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file Optional steps to setup and run Galaxy functional tests 4 - Copy test-data/* to $GALAXY_HOME/test-data/ 5 - Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that contains the tools you want to test. (e.g. 'tool_conf.xml') 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/ Configuration of Adapters ------------------------- A list of predefined adapters may be specified in the fastx_clipper_sequences.txt file which resides in the tool-data directory underneath the Galaxy root. A sample file is provided. Limitations ----------- Colorspace data support is not implemented Name adapters support is not implemented
Dependencies of this repository

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
cutadapt 1.1 package

Contents of this repository

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Name Description Version Minimum Galaxy Version
Remove adapter sequences from Fastq/Fasta 1.1.a any

Categories
Fasta Manipulation - Tools for manipulating fasta data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis