cutqc.sh is a wrapper to perform cutadapt and fastqc, and generate an aggregated report for pair-end reads, empowered by rmarkdown and plotly.

$ cutqc.sh -h
cutqc.sh in_read1.fq.gz in_read2.fq.gz out_report.html [cutadapt_option]

PLEASE REFER TO CUTADAPT AND FASTQC MANUAL ALSO.

Only pair-end gzipped input files are supported.

The first three arguments are mandatory and positional, all the other options
followed will be parsed to cutadapt, please refer to cutadapt manual.