v1.5.0

Added features:

• New dereplication mode: dereplicate by genomic neighbourhood
• Support for non-cblaster inputs from TSVs via a session construction helper tool

Improved features:

• Made hit recovery strategies synteny-aware by checking cluster layout instead of cluster contents
• Improved logging, progress bars and error catching

Tool architecture:

• Shifted to multiple class inheritance structure to define logic common to specific workflows
• Converted and integrated bash helper scripts to Python code

Miscellaneous:

• Updated examples
• Moved docs from Wiki to ReadTheDocs

What's Changed

• Synteny-aware hit recovery by @LucoDevro in #4
• Alternative input mode from TSVs by @LucoDevro in #6
• Upgrade to v1.5 by @LucoDevro in #7

Full Changelog: v1.4.5...v1.5.0

v1.4.5

Improve internal handling of cblaster binary tables to increase robustness against messy NCBI strain tags

v1.4.4

Bugfix for case when cblaster omits genomes without hits from its session file (issue #3)

v1.4.3

New features:

• Added option to use skDER's low-memory mode for the dereplication. Trades a bit of representative genome quality for much lower memory requirements and a slight speed increase.

v1.4.2

Bugfix in hit recovery

v1.4.1

Bugfix for wrongly packaged auxiliary scripts

v1.4.0 [yanked]

Complete remake in object-oriented fashion. Separate child objects for local and remote dereplication runs.

Altered features:

• Merging the dereplication status table and the assembly-scaffold pairs table into one output table (extended binary table)
• Improved verbosity

v1.3.1

Minor bugfix for excluded duplicates

v1.3.0

New features:

• Added support for cblaster local and HMM mode (for both Genbank and FASTA + GFF input genome databases).
• Expanded scaffold to assembly mapping to non-gzipped fasta files
• Added option to bypass scaffolds or assemblies to retain in the output in any case

Altered features:

• Added support for more precise ID exclusion and bypassing in case of duplicate IDs by using an assembly:scaffold ID formatting internally
• Minimum ANI threshold of 82% is now enforced: CAGEcleaner exits with a warning if a user passes a lower value.

v1.2.3

New features:

• Option to exclude scaffolds or assemblies from being processed
• Optional verbosity

Compatibility maintenance:

• Created pyproject.toml for pip compatibility