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Acknowledgments

fqxv builds on a large body of prior work in genomic and general-purpose compression. Every codec in this project is a clean-room implementation from public specifications and papers — no third-party source code is vendored — but these projects and their authors made the work possible, and we cross-checked against several of them to verify correctness.

Entropy coding

  • htscodecs — samtools/htscodecs, by James Bonfield (Genome Research Ltd), and the CRAM 3.1 codecs specification. These are the reference for our fqxv-rans (rANS Nx16) coder, the fqxv-fqzcomp quality model, and the fqxv-tokenizer read-name tokenizer.
  • rANS — Jarek Duda's work on asymmetric numeral systems, and Fabien Giesen's ryg_rans (public domain / CC0), which shaped the interleaved-state design of our rANS coder.
  • Range coding — Eugene Shelwien's range-coder design (public domain) underpins fqxv-range.
  • noodles — zaeleus/noodles, by Michael Macias — a Rust CRAM implementation we cross-checked test vectors against.

Quality-score compression

  • fqzcomp — the quality-score context model by James Bonfield that our fqxv-fqzcomp codec is modeled on.

Sequence reordering

  • SPRING — Chandak, Tatwawadi, Ochoa, Hernaez & Weissman, Bioinformatics 2019.
  • PgRC2 — Kowalski & Grabowski, Bioinformatics 2025.

These are the algorithmic references for the read-reordering engine in fqxv-reorder, reimplemented from the papers.

Long reads

  • CoLoRd — Kokot, Gudyś, Li & Deorowicz, Nature Methods 2022. The algorithmic reference for long-read compression, and the tool we measure against in Long-read support. Its platform-specific quality tables are the source of the cutpoints in our --quality-bin ont and --quality-bin hifi bins, and its edit-script approach — code each read against a similar earlier read — is the shape the fqxv-lroverlap sequence work follows.
  • minimap2 — Heng Li, Bioinformatics 2018. Its minimizer indexing and colinear-anchor chaining are the proven recipe for finding overlaps through a noisy channel; fqxv-lroverlap's chainer follows that shape.
  • miniasm — Heng Li, Bioinformatics 2016. The overlap–layout–consensus reference we checked our assembly's collapse against.
  • NanoSpring — approximate-assembly long-read sequence compression; field context for the same lever (overlap index → align → consensus graph).

As with everything else here, these are reimplemented from the published papers — no CoLoRd, minimap2, or miniasm source is vendored or translated.

Licenses

All of the above are permissive (BSD 3-Clause / MIT) or public domain and impose no obligations beyond attribution. See THIRD-PARTY-NOTICES.md in the repository for the full attribution and license details. fqxv itself is dual-licensed MIT OR Apache-2.0.