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Scythe-adapter-trimming

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

App Creator

Roger Barthelson

Quick Start

To use Scythe-adapter-trimming, import your data in FASTQ format.
Resources: Scythe README (code repository)

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 as the input file and 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 .

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.

Scythe-adapter-trimming (archived)