btrim 

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Quality trimming of nucleotide sequences (using a sliding window) in a FASTQ file. This version takes a single input file and does quality trimming only (No adapter search).

Quick Start

• To use btrim, import your data in fastq format.
• Resources: http://graphics.med.yale.edu/trim/readme

Test Data

Input File(s)

Use jumpcorr.A.fastq 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:

Select input file: /iplant/home/rogerab/testfiles/jumpcorr.A.fastq
Sliding window size: Integer 5
Quality score: Integer 15
Minimum sequence length: Integer 25
Sanger/Illumina 1.9 (PHRED+33): Flag true

Output File(s)

Expect a fastq file named after the input files as output. For the test case, the output file you will find in the example_data directory is named jumpcorr.A-trimming.fastq.

Tool Source for App

•  http://graphics.med.yale.edu/trim/