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.

UPCOMING MAINTENANCE

CyVerse systems will be unavailable, as follows:

Access to ALL CyVerse systems will be impacted during network equipment upgrades of core network equipment upgrades from Sunday, May 28 at 12 Midnight to Monday, May 29 at 8:00 AM (check your local timezone here).

CyVerse will perform regular maintenance on key systems on Tuesday, May 30 from 8 AM to 4 PM MST. Access to or usage of the following services will be unavailable or disrupted:

  • Discovery Environment: Currently running analyses will be terminated. Please plan accordingly.
  • Data Store: Unavailable during the maintenance period.
  • Atmosphere: Atmosphere instances will continue to run, but access to instances or to the web interface will be unavailable.
  • Agave/Science API: Unavailable during the maintenance period.
  • CyVerse User Portal: Unavailable during the maintenance period.

Please contact suppport@cyverse.org for any questions or concerns.

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