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

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

Skip to end of metadata
Go to start of metadata

btrim 

Community rating: ?????

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

Test Data

Icon

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

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

  • No labels