The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

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This App has been deprecated.

The newest version of this app is available here:


Scythe will identify adapter or primer sequences in your reads and remove them.

App Creator

Roger Barthelson

Quick Start

Test Data


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

Input File(s)

Use sabreN_1.fq as the input file and 454humcontamins.fa as the adapter file from the directory above as test input.

Parameters Used in App

Scythe trims, but does not remove reads, so it can be used with individual paired end files and with interlaced paired read files without the need for repair.

It is essential to provide the correct quality type (Sanger, Illumina, or Solexa. Default is Illumina) or Scythe will fail.

The minimum size of a matching sequence can be entered, and the default is 0. 

The adapter/primer sequences identified are output in the matches file.

Output File(s)

Expect a FASTQ file as output. For the test case, the output file you will find in the example_data directory is named N_sabre_scythe.fq.

Tool Source for App

The author of the application is Vince Buffalo. He has his contact information, the code, and some information about scythe posted on GitHub.

Related Tutorials

For more information about Scythe and pre-processing sequences, please visit the Pre-processing Sequencing Reads on the CyVerse Wiki in the Genome and Transcript Assembly space or Scythe-0.991 using DE.

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