Up: Component summary
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, |
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| case2 | properties | reads | mates | (missing) | (missing) | (missing) |
|
clipR1=10, |
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| case3 | properties | reads | mates | (missing) | (missing) | (missing) |
|
runFastqc=false, |
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