v0.4.5

• Add extra list and dir arguments
• Update default appraise sequence identity to match SingleM genus-level
• Functional refactoring of scripts

Full Changelog: v0.4.4...v0.4.5

v0.4.4

• Add initial graph state to clustering search (prevents first edge removal from disconnecting a sample from its largest recover umbrella)
• Supplement recover samples with next best samples (uses relevant unique targets to rank samples)

Full Changelog: v0.4.3...v0.4.4

v0.4.3

• Changed single assembly recover samples determination. Now uses top N samples ordered by weight. Using graph structure as before produced many samples with only itself as recovery (due to branching from main group before group was smaller than N).

Full Changelog: v0.4.2...v0.4.3

v0.4.2

• Add SingleM default metapackage support to evaluate
• Add --sample-singlem-list argument
• Switch to symlinking inputs rather than copying

Full Changelog: v0.4.1...v0.4.2

v0.4.1

• Remove intermediate CoverM files when done
• Update SingleM environment to latest version (Python 3.9, default metapackage via zenodo)
• Add support for metapackage via SINGLEM_METAPACKAGE_PATH environment variable (see SingleM data)

Full Changelog: v0.4.0...v0.4.1

v0.4.0

Combined cluster and coassemble subcommands as "cockatoo coassemble".

Full Changelog: v0.3.0...v0.4.0

v0.3.0

Full Changelog: v0.2.0...v0.3.0

v0.2.0

Full Changelog: https://github.com/AroneyS/cockatoo/commits/v0.2.0