Ganon Versions Save

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

1.3.0

1 year ago
  • 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

1.2.0

1 year ago
  • 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

1.1.2

2 years ago
  • fix bugs related to accession2taxid files #194

1.1.1

2 years ago
  • fix bug with multiple databases #189

1.1.0

2 years ago
  • 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: https://github.com/pirovc/ganon/compare/1.0.0...1.1.0

1.0.0

2 years ago

same functionality but many changes in the code:

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

0.4.1

2 years ago
  • general bug fixes
  • improvements in ganon table

0.4.0

3 years ago
  • 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

0.3.4

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

0.3.3

3 years ago
  • 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