EnglishGetting StartedQuick Start

Quick Start

Create Test File

cat > sample.fastq << 'EOF'
@read_1
ACGTACGTACGTACGTACGTACGTACGTACGTACGT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@read_2
TGCATGCATGCATGCATGCATGCATGCATGCATGCA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@read_3
AAAATTTTCCCCGGGGAAAATTTTCCCCGGGGAAAA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
EOF

Compress

fqc compress -i sample.fastq -o sample.fqc -v

Output:

[2026-04-16 10:30:15] INFO: Starting compression...
[2026-04-16 10:30:15] INFO: Compression complete: 108 bytes -> 67 bytes (1.61x)

Verify

fqc verify sample.fqc

Inspect

fqc info sample.fqc

Decompress and Verify

fqc decompress -i sample.fqc -o restored.fastq
diff sample.fastq restored.fastq
# No output = identical files

Use -t 8 or --threads 8 for parallel compression on multi-core systems.

Advanced Examples

Paired-End Compression

# Separate files
fqc compress -i reads_1.fastq -2 reads_2.fastq \
  -o paired.fqc --paired -t 8
 
# Interleaved
fqc compress -i interleaved.fastq -o paired.fqc --paired

Random Access

# Extract reads 1000-2000 only
fqc decompress -i archive.fqc --range 1000:2000 -o subset.fastq
 
# Extract first 5000 reads
fqc decompress -i archive.fqc --range :5000 -o first_5k.fastq
 
# Extract from read 10000 to end
fqc decompress -i archive.fqc --range 10000: -o tail.fastq

Compressed Input

# Read directly from .gz, .bz2, .xz
fqc compress -i reads.fastq.gz -o reads.fqc -t 8
fqc compress -i reads.fastq.bz2 -o reads.fqc
fqc compress -i reads.fastq.xz -o reads.fqc

Restore Original Order

fqc decompress -i archive.fqc -o restored.fastq --original-order
InstallationCore Algorithms