Implementations
16 What changed
If you have read this book before, start here.
This page is generated from the changed field of every record in the tool registry, which is filled in during each review pass. It is the same list the refresh produces, so the book’s changelog and the maintenance workflow are one artifact rather than two things to keep in sync.
- BWA-MEM2 (2026-08) — Index size caveat revised: upstream reports the on-disk index down about eightfold and the memory footprint about fourfold from earlier releases.
- STAR (2026-08) — Status moved from active to dormant. The last release is 2.7.11b (January 2024) and master has not moved since; the tool is still correct and still the default, but it is no longer releasing. Rationale re-sourced to STAR’s manual, which claims less for two-pass mode than this entry did.
- HISAT2 (2026-08) — Status corrected from dormant to active. v2.2.2 (January 2026) and v2.2.3 (July 2026) ended the gap after v2.2.1 in July 2020.
- strobealign (2026-08) — First release corrected to 2021; the paper’s read-length threshold is 150 nt, not 100 bp.
- FASTX.jl (2026-08) — Version corrected to 2.1.7. Julia packages register from git tags, and this one publishes no GitHub Release for its newest version, so the registry had been reading a stale 2.1.6.
16.1 How often this is revised
Concept chapters are revised when the science moves, which is rarely.
Implementation chapters carry their own review date in the header. A review pass checks each record’s upstream release, confirms the verdict still holds, and fills in what moved. Entries whose review date has gone stale are flagged at build time rather than left to be noticed by a reader.