Trimmomatic-programmable-0.33

Trimmomatic-programmable-0.33

Description and Quick Start

This app provides access to all trimmers that Trimmomatic can use. It uses a line-by-line text file for programming the trimming profile.

Test Data

/iplant/home/shared/iplantcollaborative/example_data/trimmomatic-0.33/inputs 

Input File(s)

A folder of fastq sequencing files, a plain text file with trimmer settings entered line by line, and an optional file of adapter or primer sequences. 

Parameters Used in App

Sample trimmer settings include:

HEADCROP:7

ILLUMINACLIP:Adapters.fa:2:30:10

SLIDINGWINDOW:4:15

MINLEN:45

Output File(s)

The output is a folder named trimout with renamed fastq files with trimmed sequences.

References

• https://github.com/timflutre/trimmomatic
• http://www.usadellab.org/cms/?page=trimmomatic