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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-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
Info |
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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.
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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
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