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Features
^^^^^^^^
- Added option to download the GUNC_DB file
- Added option to merge GUNC output with checkM output
- Added option to create interactive HTML based visualisation
- Added option to run all fastas in a directory
- Added option to provide input filepaths in a file
- Added min_mapped_genes option so scores are not calculated when there are not enough genes
- Added use_species_level option for determining tax_level with maxCSS score
- Can now accept gzipped fna files (with .gz ending)
- Allow GUNC_DB to be supplied using an env var
- Updated arguments to a subcommand structure
- Complete rewrite of how scores are calculated
- Gene calling is now done in parallel
Bugfixes
^^^^^^^^
- genome2taxonomy was not included in pip package
- GUNC failed if nothing left after minor clade filtering
- If duplicate filenames were in input, output files were overwritten
- Inputs that dont map any genes to GUNC_DB were silently missing in output
Other
^^^^^
- Documentation updates
- sklearn dependency removed
- Added the bioconda recipe to repo
- Added check for zgrep, prodigal and diamond
- Changed output names to match those in paper
- Fixed diamond version to 2.0.4 (needs to be compatable with GUNC_DB)
- Better quality LOGOs
- Diamond logs are silenced
- Timestamps added to log output
Initial Release v0.1.2 (2020-10-14)
-----------------------------------
- First release