Ganon Versions Save

• --input-target sequence support with --filter-type hibf
• improved --input-file parsing with more documentation #282
• parse acc2txid files in chunks, keeping low memory consumption on python side
• added parameterized tests for --filter-type ibf/hibf on python side

Thanks @jfy133 for reporting!

Bug fixes:

• GTDB new file formats #276
• build symbolic link overwrite #279
• Skip taxonomy reporting #280
• updated documentation

Thanks @ksavhughes and @marade for reporting

ganon2 is here (v2.0.0)

ganon2 comprises all features implemented incrementally over the years since version 1.0.0. See the releases page for a full history of changes. ganon2 is faster and uses less memory to index and to classify sequences mainly due to the use of the HIBF from raptor and the use of the amazing SeqAn3 library. ganon2 achieves good results due many factors implemented over time, like the EM-algorithm, data-based optimization of parameters, among many others.

Changes from v1.9.0:

• ganon classify --multiple-matches em/lca to choose the algorithm to solve reads with multiple-matches. --reassign option was removed, replaced by --multiple-matches em
• the output file with solved reads has now the extension .one (before .lca in ganon classify and .all in ganon reassign)
• ganon classify can now better control the integrated report generated at the end with --report-type --ranks --min-count and --skip-report
• ganon build and build-custom now generate an HIBF by default with --level species by default on ganon build. The boolean --hibf was removed and --filter-type ibf/hibf introduced.
• Updated to SeqAn3.3.0 and raptor v3.0.1 with some performance improvements (GCC >=11 required).
• Bugfixes and improved documentation

#260

#258

• Filter for false positive of a query in ganon classify with --fpr-query
• new arg --representative-genomes in ganon build
• new arg --binning in ganon classify
• new --skip-genome-size in ganon build build-custom report to not generate genome sizes in the db
• better raptor integration (v3.0.0)
• better documentation
• updated genome_updater to 0.6.3
• some bugs fixed

• New documentation with more examples and infos: https://pirovc.github.io/ganon/
• ganon classify better support for long reads
• ganon build --input-recursive to find files recursively
• ganon build --min-length to skip small sequences
• ganon build --input-target sequence performance improved
• support latest GTDB R214 release
• overall improvements and bug fixes

• fix bug #244
• update dependencies

• Optionally solves reads with multiple matches with an EM algorithm (ganon classify --reassign or ganon reassign)
• Full HIBF support from the newest raptor
• Bug fixes

• improved test coverage
• improved filter size calculation based on --max-fp or --filter-size
• new --mode on ganon build and ganon build-custom to better control filter trade-off of speed and size
  • By default --mode avg is used and will balance speed (number of bins created) and size of the final filter
  • --mode faster creates a slightly larger filter with faster classification speeds
  • --mode fastest creates a larger filter with even faster classification speeds
  • --mode smaller creates a slightly smaller filter with slower classification speeds
  • --mode smallest creates the smallest as possible filter with higher impact on classification speeds
  • when --filter-size is used instead of --max-fp, smaller/smallest control to the false positive rate instead of the size