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CLI reference

fqc exposes four top-level commands:

  • compress
  • decompress
  • info
  • verify

Global options:

Option Meaning
-t, --threads thread count (0 means auto)
-v, --verbose increase log verbosity
-q, --quiet suppress non-error output
--memory-limit memory budget in MB (0 means automatic memory selection)
--no-progress disable progress summaries

compress

fqc compress -i INPUT -o OUTPUT [OPTIONS]
Option Meaning
-2, --input2 second FASTQ file for paired-end input
-l, --level compression level 1..9 (default: 5)
`--reorder <true false>`
--streaming disable reordering and process input incrementally
--lossy-quality none, illumina8, qvz, or discard
--long-read-mode auto, short, medium, or long
--interleaved treat input as interleaved paired-end FASTQ
--max-block-bases cap per-block bases for medium and long reads
--scan-all-lengths inspect the full input instead of sampled reads for length detection
--pipeline use the staged compression pipeline
--pe-layout interleaved or consecutive metadata for paired-end archives
-f, --force overwrite output if it exists

Notes:

  • archive mode keeps the full read set in memory for global analysis and optional reordering
  • --memory-limit 0 uses automatic memory selection based on available system memory
  • for explicit low-memory runs, prefer --streaming
  • pipeline mode remains a staged execution path, not a strict low-memory ingest mode

decompress

fqc decompress -i INPUT -o OUTPUT [OPTIONS]
Option Meaning
--range extract a read range such as 1:1000 or 100:
--header-only write only read headers
--original-order restore original read order if reorder metadata exists
--skip-corrupted continue when a block fails integrity checks
--corrupted-placeholder placeholder sequence for skipped blocks
--split-pe write paired-end output to separate files
--pipeline use the staged decompression pipeline
-f, --force overwrite output if it exists

info

fqc info -i INPUT [--json] [--detailed] [--show-codecs]
  • --json emits machine-readable archive metadata
  • --detailed shows block index entries
  • --show-codecs reports codec bytes per block

verify

fqc verify -i INPUT [--quick] [--fail-fast] [--verbose]
  • --quick checks archive framing and global checksum without block decompression
  • --fail-fast stops at the first failing block
  • --verbose prints per-block verification progress