Bibliography
This bibliography is intentionally mixed: it includes external papers and project pages, but also the internal specifications and RFCs that define what FastQTools may claim today. That is the right reading posture for this project, because architecture and benchmark policy are part of the public technical story.
FASTQ and quality-score background
Use these sources to ground format assumptions and quality-score terminology before comparing tools.
Primary background on FASTQ structure, variant history, and quality-score encoding assumptions.
Useful whenever documentation needs to distinguish record structure from downstream QC policy.
Maintained scope for stat/filter capabilities, supported predicates, mutators, and representative performance targets.
This is the boundary document for what the docs may claim today.
Execution, memory, and evidence policy
These references explain why throughput claims in the whitepaper are tied to architecture and benchmark maintenance.
Defines the layered architecture, zero-copy batch model, and oneTBB pipeline rationale.
Primary source for source → processing → sink and public API boundaries.
Documents object-pool reuse and bounded batch lifecycle assumptions.
Use this when discussing memory discipline instead of speaking only in generic terms.
Formalizes benchmark collection, report generation, and regression detection thresholds.
Explains where benchmark-report data comes from and how it is stored.
Separates release-facing SLA language from informational GitHub Pages benchmark publication.
Use this to avoid overstating benchmark snapshots as universal guarantees.
- LibraryoneTBB documentation
Official documentation for parallel_pipeline and related execution primitives used in the processing path.
Helpful when mapping FastQTools stages to the underlying concurrency model.
Adjacent QC and preprocessing tools
These projects are the most useful comparison points when explaining what FastQTools is and is not trying to become.
- ProjectFastQC
Report-oriented quality-control tool focused on analysis summaries and visual inspection.
Useful contrast when discussing report-first versus embeddable processing-first boundaries.
- Projectfastp
Integrated FASTQ preprocessing tool with filtering, trimming, and report generation in one executable.
Strong comparison point for “all-in-one preprocessing” versus a narrower QC toolkit boundary.
- ProjectCutadapt
Adapter-focused trimming tool with a mature workflow and ecosystem footprint.
Relevant when explaining how FastQTools handles trimming without making adapter handling its only narrative.
- Projectseqtk
Compact FASTA/FASTQ command-line toolkit with Unix-style ergonomics and low ceremony.
Good contrast for readers who value compact utilities over a layered whitepaper + API story.
Citation protocol
Use this list in layers:
- start with FASTQ and QC background sources when terminology needs formal grounding;
- move to architecture and benchmark RFCs when the claim concerns execution policy, memory discipline, or publication posture;
- finish with adjacent project references when the goal is comparison rather than implementation detail.
How to use this list
Treat the bibliography as the canonical citation surface for the whitepaper, not as a miscellaneous link dump. If a chapter makes a strong comparative or methodological claim, the supporting source should be recoverable from here.
Citation quality bar
The bibliography is maintained with the same claim discipline as the rest of the whitepaper:
- a source must support a concrete claim about format, execution policy, benchmark interpretation, or adjacent-tool context;
- internal RFCs are valid citations because they define what FastQTools is allowed to claim;
- project pages are used for comparison context, not for borrowing unsupported capability claims;
- benchmark citations should always be paired with method or policy references.