CLI Usage Reference

fqc compress [OPTIONS] -i <input> -o <output>

# Basic
fqc compress -i reads.fastq -o reads.fqc
 
# Parallel
fqc compress -i reads.fastq -o reads.fqc -t 8
 
# Best quality
fqc compress -i reads.fastq -o reads.fqc --mode best
 
# Paired-end
fqc compress -i r1.fastq -2 r2.fastq -o paired.fqc --paired
 
# From compressed input
fqc compress -i reads.fastq.gz -o reads.fqc

fqc decompress [OPTIONS] -i <input> -o <output>

# Full
fqc decompress -i reads.fqc -o restored.fastq
 
# Partial
fqc decompress -i reads.fqc --range 1000:2000 -o subset.fastq
 
# Original order
fqc decompress -i reads.fqc -o restored.fastq --original-order

fqc info [OPTIONS] <archive>

fqc verify <archive>

fqc split-pe -i <input> -1 <out1> -2 <out2> [--range <range>]