Up: Component summary Component

QCParser

Parse SeqQC summary result.

Version 1.0
Bundle sequencing
Categories Quality control
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml QCParser.pl
Usage Example with default values

Inputs

Name Type Mandatory Description
summary Array<BinaryFile> Mandatory FASTQ file containing unpaired reads or the #1 mates for paired-end input.

Outputs

Name Type Description
basicStats Array<CSV> Basic stats. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
perBaseSeqQual Array<CSV> Per base sequence quality. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
perSeqQualScore Array<CSV> Per sequence quality scores. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
perBaseSeqContent Array<CSV> Per base sequence content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
perBaseGC Array<CSV> Per base GC content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
perSeqGC Array<CSV> Per sequence GC content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
perBaseN Array<CSV> Per base N content. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
seqDuplicateLevel Array<CSV> Sequence duplicate levels. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.
overrepresented Array<CSV> Overrepresented sequences. For pair-end data, the keys are 'read' and 'mate'. For single-end data, the key is 'read'.

Parameters

Name Type Default Description
paired boolean true A boolean for pair-end data. The default is: true.

Test cases

Test case Parameters IN
summary
OUT
basicStats
OUT
perBaseSeqQual
OUT
perSeqQualScore
OUT
perBaseSeqContent
OUT
perBaseGC
OUT
perSeqGC
OUT
perBaseN
OUT
seqDuplicateLevel
OUT
overrepresented
case1 (missing) summary basicStats perBaseSeqQual perSeqQualScore perBaseSeqContent perBaseGC perSeqGC perBaseN seqDuplicateLevel overrepresented
case2 properties summary basicStats perBaseSeqQual perSeqQualScore perBaseSeqContent perBaseGC perSeqGC perBaseN seqDuplicateLevel overrepresented

paired=false

case3 properties summary basicStats perBaseSeqQual perSeqQualScore perBaseSeqContent perBaseGC perSeqGC perBaseN seqDuplicateLevel overrepresented

paired=false


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