A pipeline to process and QC sRNA sequence data: screens out low-quality reads, trims adapter sequences and generates a FastQC report.
Written in bash.
Requires:
fastq_quality_filter
cutadapt
fastx_collapser
FastQC
Basic usage is:
sRNAQC.sh -i reads.fastq
sRNAQC accepts the following additional arguments (all of which have defaults already set):
-a (3' adapter sequence)
-c (number of cores, default=1)
-n (number of ambiguities in 3' adapter sequence, default=0)
-h display help message