This App has been deprecated.
The newest version of this app is available here: https://de.cyverse.org/de/?type=apps&app-id=8656db68-64d8-11e6-ac4f-008cfa5ae621&system-id=de
Scythe will identify adapter or primer sequences in your reads and remove them.
- To use Scythe-adapter-trimming, import your data in FASTQ format.
- Resources: Scythe README (code repository)
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.
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.
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.