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Quality control

Description Short reads quality control.
Component Version Inputs Outputs Description
FastQC 2.0 read, mate summary, report, extra, folder Short reads quality control for high-throughput sequencing data.
QCFasta 5.0 reads, mates, fastQCfolders, adapter qcReads, qcMates, report, table, qcUnpairedReads, qcUnpairedMates Quality control function for high-throughput sequencing data.
QCParser 1.0 summary basicStats, perBaseSeqQual, perSeqQualScore, perBaseSeqContent, perBaseGC, perSeqGC, perBaseN, seqDuplicateLevel, overrepresented Parse SeqQC summary result.
TrimGalore 1.1 reads, mates trimmed, report, stats 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.
Trimmer 1.0 data, perBaseSeqQual, trimInfo trimmedReads Trim sequence reads at both ends.
Trimmomatic 2.1 read, mate, adapter trimmedReads, stdout, stats, log Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

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