Central thesis
fq-compressor gets its identity from the interaction between assembly-inspired sequence reduction, dedicated quality modeling, and an archive format that keeps direct lookup viable.
Algorithms whitepaper
The whitepaper lane explains the compression thesis behind fq-compressor without turning the public docs into an implementation notebook. Read it as a systems argument about why short-read redundancy, block structure, and retrieval semantics can coexist in one archive design.
Boundary condition
The whitepaper is intentionally paired with the performance section. Design claims may be ambitious, but public positioning is kept inside the evidence surface the repository can reproduce today.
Dossier map
| Dossier | Core question | Why it matters |
|---|---|---|
| ABC pipeline | How are reads grouped and reduced before archive write-out? | Explains the main sequence-side compression lever |
| SCM quality modeling | Why are quality values handled as their own probabilistic stream? | Shows why ratio and throughput trade-offs are not sequence-only |
| Read reordering | Why change input order if the archive must remain reversible? | Frames locality as a compression tool rather than a preprocessing trick |
| Consensus and delta representation | Why encode one local consensus plus sparse edits? | Connects assembly-style reasoning to block-local storage |
Questions this section should answer
- Why does fq-compressor treat read ordering as a first-class operation rather than a hidden optimization?
- Why are sequence, ID, and quality transforms separated instead of collapsed into one opaque codec?
- Which pieces of the design are inherited from literature such as SPRING [R1], and which are specific to fq-compressor's archive contract?
Continue with
- System Design for module boundaries and archive responsibilities
- Performance for the current public proof surface
- References for the bibliography and comparator shelf