Trimmomatic: Paired End (PE)¶

trimmomaticPairedEnd · 1 contributor · 1 version

Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem depending on the library preparation and downstream application.

There are two major modes of the program: Paired end mode and Single end mode. The paired end mode will maintain correspondence of read pairs and also use the additional information contained in paired reads to better find adapter or PCR primer fragments introduced by the library preparation process.

Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used). Files compressed using either “gzip” or “bzip2” are supported, and are identified by use of “.gz” or “.bz2” file extensions.

Quickstart¶

from janis_bioinformatics.tools.usadellab.trimmomatic.versions import TrimmomaticPairedEnd_0_35

wf = WorkflowBuilder("myworkflow")

wf.step(
    "trimmomaticpairedend_step",
    TrimmomaticPairedEnd_0_35(
        steps=None,
        sampleName=None,
        inp=None,
    )
)
wf.output("pairedOut", source=trimmomaticpairedend_step.pairedOut)
wf.output("unpairedOut", source=trimmomaticpairedend_step.unpairedOut)

OR

Install Janis
Ensure Janis is configured to work with Docker or Singularity.
Ensure all reference files are available:

Note

More information about these inputs are available below.

Generate user input files for trimmomaticPairedEnd:

# user inputs
janis inputs trimmomaticPairedEnd > inputs.yaml

inputs.yaml

inp:
- inp_0.fastq.gz
- inp_1.fastq.gz
sampleName: <value>
steps:
- <value>
- <value>

Run trimmomaticPairedEnd with:

janis run [...run options] \
    --inputs inputs.yaml \
    trimmomaticPairedEnd

Information¶

ID:	`trimmomaticPairedEnd`
URL:	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
Versions:	0.35
Container:	quay.io/biocontainers/trimmomatic:0.35–6
Authors:	illusional
Citations:	Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.
DOI:	10.1093/bioinformatics/btu170
Created:	2020-05-25
Updated:	2020-05-25

Outputs¶

name	type	documentation
pairedOut	FastqGzPair
unpairedOut	FastqGzPair

Additional configuration (inputs)¶

name	type	prefix	position	documentation
steps	Array<String>		100	ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read. SLIDINGWINDOW: Performs a sliding window trimming approach. It starts scanning at the 5” end and clips the read once the average quality within the window falls below a threshold. MAXINFO: An adaptive quality trimmer which balances read length and error rate to maximise the value of each read 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 by removing bases from the end HEADCROP: Cut the specified number of bases from the start of the read MINLEN: Drop the read if it is below a specified length AVGQUAL: Drop the read if the average quality is below the specified level TOPHRED33: Convert quality scores to Phred-33 TOPHRED64: Convert quality scores to Phred-64
sampleName	String			Used to name the output
inp	FastqGzPair		5
threads	Optional<Integer>	-threads	2
phred33	Optional<Boolean>	-phred33	3	Use phred + 33 quality score. If no quality encoding is specified, it will be determined automatically
phred64	Optional<Boolean>	-phred64	3	Use phred + 64 quality score. If no quality encoding is specified, it will be determined automatically
trimLogFilename	Optional<Filename>	-trimlog	4	Specifying a trimlog file creates a log of all read trimmings, indicating the following details: the read name the surviving sequence length the location of the first surviving base, aka. the amount trimmed from the start the location of the last surviving base in the original read the amount trimmed from the end
outputFilename_R1	Optional<Filename>		6
outputFilenameUnpaired_R1	Optional<Filename>		7
outputFilename_R2	Optional<Filename>		8
outputFilenameUnpaired_R2	Optional<Filename>		9

Workflow Description Language¶

version development

task trimmomaticPairedEnd {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[String] steps
    String sampleName
    Int? threads
    Boolean? phred33
    Boolean? phred64
    String? trimLogFilename
    Array[File] inp
    String? outputFilename_R1
    String? outputFilenameUnpaired_R1
    String? outputFilename_R2
    String? outputFilenameUnpaired_R2
  }
  command <<<
    set -e
    trimmomatic \
      'PE' \
      ~{if defined(threads) then ("-threads " + threads) else ''} \
      ~{if (defined(phred33) && select_first([phred33])) then "-phred33" else ""} \
      ~{if (defined(phred64) && select_first([phred64])) then "-phred64" else ""} \
      -trimlog '~{select_first([trimLogFilename, "trimlog.log"])}' \
      ~{if length(inp) > 0 then "'" + sep("' '", inp) + "'" else ""} \
      '~{select_first([outputFilename_R1, "~{sampleName}-_R1.trimmed.fastq.gz"])}' \
      '~{select_first([outputFilenameUnpaired_R1, "~{sampleName}-_R1.unpaired.fastq.gz"])}' \
      '~{select_first([outputFilename_R2, "~{sampleName}-_R2.trimmed.fastq.gz"])}' \
      '~{select_first([outputFilenameUnpaired_R2, "~{sampleName}-_R2.unpaired.fastq.gz"])}' \
      ~{if length(steps) > 0 then "'" + sep("' '", steps) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/trimmomatic:0.35--6"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    Array[File] pairedOut = glob("*trimmed.fastq.gz")
    Array[File] unpairedOut = glob("*unpaired.fastq.gz")
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'Trimmomatic: Paired End (PE)'
doc: |-
  Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop
  Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem
  depending on the library preparation and downstream application.

  There are two major modes of the program: Paired end mode and Single end mode. The
  paired end mode will maintain correspondence of read pairs and also use the additional
  information contained in paired reads to better find adapter or PCR primer fragments
  introduced by the library preparation process.

  Trimmomatic works with FASTQ files (using phred + 33 or phred + 64 quality scores,
  depending on the Illumina pipeline used). Files compressed using either "gzip" or "bzip2" are
  supported, and are identified by use of ".gz" or ".bz2" file extensions.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/trimmomatic:0.35--6

inputs:
- id: steps
  label: steps
  doc: |
    ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
    SLIDINGWINDOW: Performs a sliding window trimming approach. It starts
    scanning at the 5" end and clips the read once the average quality within the window
    falls below a threshold.
    MAXINFO: An adaptive quality trimmer which balances read length and error rate to
    maximise the value of each read
    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 by removing bases from the end
    HEADCROP: Cut the specified number of bases from the start of the read
    MINLEN: Drop the read if it is below a specified length
    AVGQUAL: Drop the read if the average quality is below the specified level
    TOPHRED33: Convert quality scores to Phred-33
    TOPHRED64: Convert quality scores to Phred-64
  type:
    type: array
    items: string
  inputBinding:
    position: 100
- id: sampleName
  label: sampleName
  doc: Used to name the output
  type: string
- id: threads
  label: threads
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -threads
    position: 2
- id: phred33
  label: phred33
  doc: |-
    Use phred + 33 quality score. If no quality encoding is specified, it will be determined automatically
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -phred33
    position: 3
- id: phred64
  label: phred64
  doc: |-
    Use phred + 64 quality score. If no quality encoding is specified, it will be determined automatically
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -phred64
    position: 3
- id: trimLogFilename
  label: trimLogFilename
  doc: |-
    Specifying a trimlog file creates a log of all read trimmings, indicating the following details:

        - the read name
        - the surviving sequence length
        - the location of the first surviving base, aka. the amount trimmed from the start
        - the location of the last surviving base in the original read
        - the amount trimmed from the end
  type:
  - string
  - 'null'
  default: trimlog.log
  inputBinding:
    prefix: -trimlog
    position: 4
- id: inp
  label: inp
  type:
    type: array
    items: File
  inputBinding:
    position: 5
    itemSeparator: ' '
- id: outputFilename_R1
  label: outputFilename_R1
  type:
  - string
  - 'null'
  default: generated-_R1.trimmed.fastq.gz
  inputBinding:
    position: 6
    valueFrom: $(inputs.sampleName)-_R1.trimmed.fastq.gz
- id: outputFilenameUnpaired_R1
  label: outputFilenameUnpaired_R1
  type:
  - string
  - 'null'
  default: generated-_R1.unpaired.fastq.gz
  inputBinding:
    position: 7
    valueFrom: $(inputs.sampleName)-_R1.unpaired.fastq.gz
- id: outputFilename_R2
  label: outputFilename_R2
  type:
  - string
  - 'null'
  default: generated-_R2.trimmed.fastq.gz
  inputBinding:
    position: 8
    valueFrom: $(inputs.sampleName)-_R2.trimmed.fastq.gz
- id: outputFilenameUnpaired_R2
  label: outputFilenameUnpaired_R2
  type:
  - string
  - 'null'
  default: generated-_R2.unpaired.fastq.gz
  inputBinding:
    position: 9
    valueFrom: $(inputs.sampleName)-_R2.unpaired.fastq.gz

outputs:
- id: pairedOut
  label: pairedOut
  type:
    type: array
    items: File
  outputBinding:
    glob: '*trimmed.fastq.gz'
    loadContents: false
- id: unpairedOut
  label: unpairedOut
  type:
    type: array
    items: File
  outputBinding:
    glob: '*unpaired.fastq.gz'
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: trimmomatic
arguments:
- position: 0
  valueFrom: PE

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: trimmomaticPairedEnd