References

This page lists the scientific and technical references discussed in the BfxPM documentation and development plan, including international standards for reproducible research and data management.

International Guidelines & Standards

• The Turing Way - The leading international handbook for reproducible, ethical, and collaborative data science.
• ELIXIR Research Data Management (RDM) - Best practices for life science data management, emphasizing the separation of raw data and results.
• Software Carpentry (Project Organization) - Foundations of structured computational research.
• nf-core Project Structure - Guidelines for scalable, reproducible bioinformatics pipelines.
• Snakemake Best Practices - Structural recommendations for modular workflow management.
• FAIR Research Software (FAIR4RS) - International standards for making software Findable, Accessible, Interoperable, and Reusable.
• Wilkinson et al. (2016) - The foundational paper on the FAIR Guiding Principles for scientific data management and stewardship.
• Gentleman et al. (2004) - Bioconductor - Foundational concepts for open source software in bioinformatics.

CLI & Software Design Philosophy

• Command Line Interface Guidelines - An open-source guide to help you write better command-line programs.
• Rich Documentation - The library powering BfxPM's visual terminal experience.
• Typer Documentation - The framework enabling our modular and type-safe CLI structure.

Sequence Data Compression

1. Academic 0up (Lossless Genomic Compression) - General overview of essential lossless strategies.
2. PMC6662292 (Specialized Compressors) - Performance comparisons of specialized genomic compressors vs. Gzip.
3. IEEE Spectrum (The Desperate Quest for Genomic Compression) - Rationale for domain-specific algorithms.
4. Nature Scientific Reports (Lossless Compression of FASTQ Files)
5. NanoSpring (Long-read FASTQ Compression) - Specialized tool for Nanopore and PacBio data.
6. EBI Sequence File Formats
7. Biostars Thread (FASTQ vs CRAM vs Genozip)
8. Illumina FASTQ ORA Format

Aligned Data (BAM/CRAM)

1. Bioinformatics Stack Exchange (Best Archive Practices)
2. CRAM Specification (GA4GH Standard)
3. HTSeq Read Mapping Documentation

Raw Signal Data (FAST5/POD5/SLOW5)

1. Oxford Nanopore Beginner's Guide to Formats
2. SLOW5 & blow5 Documentation - Open-source lossless alternative for raw signal recording.
3. VBZ Compression Plugin - Lossless squiggle signal compression within HDF5.