Difference between revisions of "Trimmomatic"

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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|trimmomatic}}
 
|{{#vardefine:app|trimmomatic}}
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For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.
 
For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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  module load trimmomatic/0.32
 
  module load trimmomatic/0.32
  trimmomatic PE --phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
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  trimmomatic PE --phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz \
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output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \
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ILLUMINACLIP:${HPC_TRIMMOMATIC_ADAPTER}/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
 
|}}
 
|}}
 
<!--PBS scripts-->
 
<!--PBS scripts-->

Latest revision as of 20:52, 12 August 2022

Description

trimmomatic website  

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

The current trimming steps are:

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.

SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.

LEADING: Cut bases off the start of a read, if below a threshold quality

TRAILING: Cut bases off the end of a read, if below a threshold quality

CROP: Cut the read to a specified length

HEADCROP: Cut the specified number of bases from the start of the read

MINLEN: Drop the read if it is below a specified length

TOPHRED33: Convert quality scores to Phred-33

TOPHRED64: Convert quality scores to Phred-64

It works with FASTQ (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determined based on the .gz extension.

For single-ended data, one input and one output file are specified, plus the processing steps. For paired-end data, two input files are specified, and 4 output files, 2 for the 'paired' output where both reads survived the processing, and 2 for corresponding 'unpaired' output where a read survived, but the partner read did not.

Environment Modules

Run module spider trimmomatic to find out what environment modules are available for this application.

System Variables

  • HPC_TRIMMOMATIC_DIR - installation directory

Additional Information

Use the trimmomatic_se and trimmomatic_pe wrappers for trimmomatic/0.22 to run Trimmomatic for single-end and paired-end reads respectively or the trimmomatic wrapper for trimmomatic/0.32 or later. For example,

module load trimmomatic/0.32
trimmomatic PE --phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz \
output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \
ILLUMINACLIP:${HPC_TRIMMOMATIC_ADAPTER}/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36