Up: Component summary Component

TrimGalore

The component is a wrapper of the trim_galore tool which is also a wrapper of two tools: fastqc and cutadapt which both should be in PATH. Trim_galore performs quality trimming, adapter removal and runs fastqc for the trimmed reads (and mates). The first 13 bases of the illumina adapters 'AGATCGGAAGAGC' are used by default for adapter removal. The default adapters can be modified by specifying the adapter sequence in the adapter parameter. Trim_galore also support special functionalities for RRBS data by setting appropriate flags in the extraArgs parameter.

Version 1.1
Bundle sequencing
Categories Quality control
Authors Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)
Issue tracker View/Report issues
Requires trim_galore ; fastqc ; cutadapt (python)
Source files component.xml TrimGalore.bash
Usage Example with default values

Inputs

Name Type Mandatory Description
reads SequenceSet Mandatory Input reads in fastq format, can be gzipped.
mates SequenceSet Optional Input mates in fastq format, can be gzipped.

Outputs

Name Type Description
trimmed Array<FASTQ> Array of trimmed reads (key: Reads) and mates (key: Mates) in fastq format, can be gzipped based on the gzip parameter.
report BinaryFolder Folder containing quality (if runFastqc is specified) and trimming reports. This folder can be fed to SimpleWebPage component with index="fastqc_report.html".
stats CSV Summary stats

Parameters

Name Type Default Description
adapter string "" Alternative adapter to be trimmed. If Null, the default first 13 bases of Illumina adapter will be used.
clipR1 int 0 Clip the first "int" number of bases from reads input.
clipR2 int 0 Clip the first "int" number of bases from mates input.
extraArgs string "" Extra flags to be passed to trim_galore.
fastqcArgs string "" Extra flags to be passed to fastqc.
gzip boolean true Set true for gzipping the output.
minLength int 50 Minimum read length required to keep the read after trimming.
minQuality int 30 Threshold for quality trimming.
paired boolean true Set true for paired-end reads.
qualityScore string "phred33" The quality score for input files which can be "phred33" or "phred64".
runFastqc boolean true Set true for running fastqc after trimming.
stringency int 2 Overlap with adapter sequence required to trim a sequence.

Test cases

Test case Parameters IN
reads
IN
mates
OUT
trimmed
OUT
report
OUT
stats
case1 properties reads (missing) (missing) (missing) (missing)

paired=false,
minLength=20,
minQuality=20,
stringency=7,

case2 properties reads mates (missing) (missing) (missing)

clipR1=10,
clipR2=10,
extraArgs=--three_prime_clip_R1 2,
gzip=false,
extraArgs="--retain_unpaired"

case3 properties reads mates (missing) (missing) (missing)

runFastqc=false,
adapter=TCGCTC,
,


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