v1.2.0

[1.2.0] - 2026-01-05

Added

• New parallel clique-based dereplication workflow (from parallel-cliques branch) to improve scalability on large connected components
• --anifile command-line option to directly use existing skani output (avoids repeated skani runs if user wants to dereplicate genomes under different quality and ANI thresholds)
• -a/--alignedfrac command-line option to apply a fraction-aligned threshold when detecting redundant genomic pairs

Changed

• Final dereplication step in no-reassembly mode now reuses the original skani output instead of rerunning skani
• Minor refactoring to improve code readability

Performance

• Benchmarked MAGmax performance against Galah

v1.1.0

v1.1.0

New feature added

• Created no-reassembly command-line option.
• It enables dereplication of input bins without bin merging and reassembly

v1.0.0

rename and updated main to remove unnecessary options