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ganon version 2.0.0 (a.k.a. ganon2)
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@pirovc pirovc released this 17 Nov 16:38
· 14 commits to master since this release
2.0.0
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Learn about vigilant mode.

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
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