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

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HTProcess_trimmomatic_0.32

Trims reads initialized with HTProcess_fastqc for quality control, and runs fastqc on them again.

App Creator

Roger Barthelson

Quick Start

  • To use HTProcess_trimmomatic_0.32, import your data from the output of HTProcess_fastqc-0.1, or HTProcess-prepare_directories_and_run_fastqc. The input is a directory named HTProcess_reads.
  • Resources: http://www.usadellab.org/cms/?page=trimmomatic

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess_fastqc

Use the HTProcess_Reads directory

Input File(s)

Use the output directory, HTProcess_READS, from HTProcess_fastqc-0.1 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.

Headcrop Integer 12
Illuminaclip Adapter fasta file (this file is shared with program 2) Input /iplant/home/rogerab/test_dir/illumina_adapters.fa
Illuminaclip settings/seed mismatches Integer 2
Illuminaclip settings/palindrome clip threshold: Integer 25
Illuminaclip settings/simple clip threshold Integer 10
Leading Integer
Trailing Integer
Sliding Window Settings/window size Integer 4
Sliding Window Settings/average quality Integer 18
Max Info Settings/target read length Integer
Max Info Settings/strictness Double
Crop Integer
Minimum read length (shared setting with Program 2) Integer 60
Headcrop Integer
Illuminaclip settings/seed mismatches Integer
Illuminaclip settings/palindrome clip threshold: Integer
Illuminaclip settings/simple clip threshold Integer
Leading Integer
Trailing Integer
Sliding Window Settings/window size Integer
Sliding Window Settings/average quality Integer
Max Info Settings/target read length Integer
Max Info Settings/strictness Double
Crop Integer
HeadcropInteger 12

Illuminaclip Adapter fasta file (this file is shared with program 2) illumina_adapters.fa

Illuminaclip settings/seed mismatches  Integer 2

Illuminaclip settings/palindrome clip threshold Integer 25

Illuminaclip settings/simple clip threshold Integer 10

Sliding Window Settings/window size Integer  4

Sliding Window Settings/average quality Integer 18

Output File(s)

Expect as output a directory named HTProcess_Reads_T1, as well as a separate summary file for running fastqc again on all fastq files.

An example is found here:Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess_trimmomatic

Related Tutorials

Cleaning up your reads with the HTProcess Pipeline

Tool Source for App

http://www.usadellab.org/cms/?page=trimmomatic

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