Bibliography and repositories

Use this page as the citation key for the public documentation set.

Numbered literature

1. [R1] Chandak, Shubham, et al. SPRING: a next-generation compressor for FASTQ files.
   The closest paper-level framing for assembly-based compression, reversible reordering, and consensus-style sequence reduction.
2. [R2] Bonfield, James K. fqzcomp repository.
   A compact quality-value compression reference that sharpens the discussion around stream-specific coding trade-offs.
3. [R3] Sahlin, Kristoffer, et al. NanoSpring: reference-free lossless compression of nanopore sequencing reads.
   A useful long-read comparator when explaining what fq-compressor is not optimized around first.

Comparator repositories

1. [C1] shubhamchandak94/Spring
   Closest external repository for the assembly-based compression framing.
2. [C2] shubhamchandak94/HARC
   FASTQ-specialized comparator for architecture and project-scope trade-offs.
3. [C3] jkbonfield/fqzcomp
   Quality-modeling comparator that pressures fq-compressor's stream decomposition.
4. [C4] qm2/NanoSpring
   Long-read comparison target used to explain scope boundaries.

Repository-local evidence anchors

1. [E1] benchmark/results/
   Machine-readable and narrative benchmark outputs used by the performance section.
2. [E2] vendor/spring-core/
   Extracted Spring-derived reference code with an explicit license boundary.
3. [E3] ref-projects/
   Repository-local comparison targets and study notes.
4. [E4] docs/archive/
   Historical research and spec material retained for reference only.