ganon version 1.3.0

• inclusion of genome sizes on ganon build
• addition of --report-types in ganon report with support to read count re-distribution (dist) and correction by genome size (corr) or both (abundance)
• bioboxes output on ganon report --output-format bioboxes
• option to filter by --top-percentile on ganon report
• improved test coverage
• bug fixes

ganon version 1.2.0

• integrated download/update of reference sequences with genome_updater
• native NCBI and GTDB support with multitax
• new build and build-custom
  • minimizers as default
  • database files integrated (only .ibf and .tax) - incompatible with older versions
  • better integration and retrieval of NCBI data
  • smaller databases with real hash counter and multiple testing correction
• drop use of taxsbp on build
• drop absolute thresholds on classify (use --rel-cutoff and --rel-filter instead)
• experimental HIBF support on classify with raptor indices
• several fixes and improvements

ganon version 1.1.2

• fix bugs related to accession2taxid files #194

ganon version 1.1.1

• fix bug with multiple databases #189

ganon version 1.1.0

• With minimizer support
• Improved filter size estimation
• Auto hash function estimation
• Simplified threshold calculations
• Better handling of cutoff and filter, absolute or relative:
  • --max-error now --abs-cutoff
  • --min-kmers now --rel-cutoff
  • --strata-filter now --abs-filter
  • new --rel-filter
• --max-error-unique removed
• Overall faster and more stable code

Full Changelog: 1.0.0...1.1.0

ganon version 1.0.0

same functionality but many changes in the code:

• now using seqan3 insetad of seqan2
• several bug fixes and code improvements
• more info at #181

ganon version 0.4.1

• general bug fixes
• improvements in ganon table

ganon version 0.4.0

• customized specialization options on build and update (file, sequence, assembly, custom)
• sorted output on ganon-get-seq-info.sh
• integration with taxsbp 1.1.1
• general improvements and fixes

ganon version 0.3.4

• advanced options on ganon report and ganon table
• bugfix retrieving assembly accession from ncbi

ganon version 0.3.3

• improved report function with more filters and functionalities
• removal of species+ reporting
• reports can be generated with external taxdump and multiple filters
• ganon table function to summarize multiple reports