Difference between revisions of "Trimmomatic"
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=Introduction= | =Introduction= | ||
| − | = Example use-cases= | + | Another tool for quality trimming ... this is probably the best known. |
| + | |||
| + | = Usage = | ||
| + | |||
| + | Trimmomatic is quite unique in the way it is called. | ||
| + | |||
| + | It is a java program, so this requires the jar file naturally, and then: | ||
| + | |||
| + | # whether single- or pair-end reads (SE|PE) | ||
| + | # number of threads with hyphen, i.e. -threads N | ||
| + | # whether quality scoring is phred33 or phred64 (although it will try to detect) | ||
| + | |||
| + | * $TS3SE is TruSeq3-SE.fa | ||
| + | * $TS2SE is TruSeq2-SE.fa | ||
| + | * $TS2PE is TruSeq2-PE.fa | ||
| + | * $NXPE is NexteraPE-PE.fa | ||
| + | * $TS3PE is TruSeq3-PE.fa | ||
| + | * $TS3PE2 is TruSeq3-PE-2.fa | ||
| + | |||
| + | |||
| + | == Example use-cases== | ||
java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50 | java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50 | ||
Revision as of 14:54, 5 July 2016
Introduction
Another tool for quality trimming ... this is probably the best known.
Usage
Trimmomatic is quite unique in the way it is called.
It is a java program, so this requires the jar file naturally, and then:
- whether single- or pair-end reads (SE|PE)
- number of threads with hyphen, i.e. -threads N
- whether quality scoring is phred33 or phred64 (although it will try to detect)
- $TS3SE is TruSeq3-SE.fa
- $TS2SE is TruSeq2-SE.fa
- $TS2PE is TruSeq2-PE.fa
- $NXPE is NexteraPE-PE.fa
- $TS3PE is TruSeq3-PE.fa
- $TS3PE2 is TruSeq3-PE-2.fa
Example use-cases
java -jar $PATHTRIMMOJAR/trimmomatic-0.32.jar PE -threads 6 -phred33 $DATASETPATH/Pair1.fastq.gz $DATASETPATH/Pair1.fastq.gz forward_paired.fq forward_unpaired.fq reverse_paired.fq reverse_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50
