cutadapt

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cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

Quick Start

To use cutadapt, import your data in FASTQ or fastq.gz format.
Resources: http://code.google.com/p/cutadapt/
https://github.com/marcelm/cutadapt

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> cutadapt.

Input File(s)

Use illumina.fastq or illumina.fastq.gz from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Default parameters only, no further configuration needed.

Output File(s)

Expect a text file named outputForCutadapt.txt with a summary of the clipped sequences and the modified FASTQ file (output.fastq) as output.

Tool Source for App

http://code.google.com/p/cutadapt/