CLI workflows

This page keeps the operational command set compact. For implementation context, read Architecture. For exact repository evidence and related work, use Research.

Global options

Apply these before the subcommand:

• -t, --threads <n>: set worker count (0 means auto)
• -v, --verbose: increase log verbosity
• -q, --quiet: suppress non-error output
• --memory-limit <MB>: cap memory budget
• --no-progress: disable progress display
• --log-file <path> / --log-level <level>: redirect or tune logging
• --json: JSON output for info and verify
• -V, --version: print version

Compress

fqc compress -i reads.fastq -o reads.fqc

Useful options:

• -2, --input2 <path>: second FASTQ for paired-end input
• --paired: paired-end mode
• --interleaved: paired-end reads already interleaved in one file
• -l, --level <1-9>: compression level
• --preserve-order or --no-reorder: disable global reordering
• --streaming: stdin-friendly mode with lower compression potential
• --quality-mode <lossless|illumina8|discard>
• --id-mode <exact|tokenize|discard>
• --long-read-mode <auto|short|medium|long>
• --block-reads <n> / --max-block-bases <n>: block sizing controls
• -f, --force: overwrite an existing output file

Examples:

fqc compress -i reads.fastq.gz -o reads.fqc -t 8
fqc compress -i r1.fastq -2 r2.fastq -o paired.fqc --paired
fqc compress -i - -o stream.fqc --streaming

Decompress

fqc decompress -i reads.fqc -o restored.fastq

Useful options:

• --range <start:end>: extract a read interval
• --range-pairs <start:end>: extract paired-end intervals in pair units
• --original-order: rebuild original order when a reorder map is present
• --header-only: output identifiers only
• --streams <all|id|seq|qual|...>: decode selected streams
• --output-format <fastq|fasta|tsv|raw>
• --split-pe: split paired-end output
• --skip-corrupted: continue past corrupted blocks
• --verify / --no-verify: control checksum verification during decode

Examples:

fqc decompress -i reads.fqc --range 1:1000 -o subset.fastq
fqc decompress -i paired.fqc -o restored.fastq --original-order
fqc decompress -i archive.fqc -o headers.txt --header-only

Inspect and verify

fqc info -i reads.fqc
fqc verify -i reads.fqc

Useful options:

• fqc info --json --detailed --show-index --show-codecs
• fqc verify --mode quick
• fqc verify --fail-fast --json

Operator pattern

fqc compress -i reads.fastq -o reads.fqc -t 8
fqc verify -i reads.fqc
fqc info -i reads.fqc --show-index
fqc decompress -i reads.fqc --range 1001:2000 -o spot-check.fastq

Continue with

• Getting started for a first verified run
• Contributing for repo checks and documentation updates
• Research references for adjacent papers and compressors