Version 1.9.0

Important Notes:

• Beginning with Version 1.8.0, the macOS binary provided by the BISCUIT maintainers will be built for the Apple M-series (arm64) CPU. For those with macOS using an Intel (x64_64) CPU, BISCUIT is available through bioconda or can be built from source.
• Beginning with Version 1.4.0, BISCUIT no longer needs submodules. Therefore, the GitHub-generated Source code (zip) and Source code (tar.gz) links may contain all necessary files. If preferred, release-source.zip is guaranteed to contain all BISCUIT source files.
• Beginning with Version 1.0.0, BISCUIT is no longer backwards compatible with Version 0.3.16 and earlier.

Date Created:

• 24 June 2026

General Changes:

• Updates to testing framework.

Changes affecting specific subcommands/scripts:

• align:
  • Prior to this release, BISCUIT treated unplaced or unlocalized contigs as ALT contigs. Now, it relies solely on the ref.fa.alt file to define which contigs will be treated as ALTs. This change may result in alignment positions; however, initial tests show this to be a small effect (~1-3%).
  • -i option dropped as this is now the default behavior of BISCUIT.

Bug Fixes:

• Issue #76 point 1 addressed. (Differences when aligning WGS with BISCUIT in part due to treatment of unplaced/unlocalized contigs). Reported by lh3.
• Issue #76 point 2 fixed. (Incorrect insert size calculation during mate rescue).