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Update Log

v1.2.0

Major updates

  • New k-mer format introduced.
    • Older databases are still compatible, but not recommended.
    • Older Metabuli versions are not compatible with the new database format.
  • New options in build module
    • --syncmer: Use syncmers instead of all k-mers.
      • It reduces the database size and classification speed.
      • Reduction rate (k - s + 1) / 2 can be specified using --smer-len to set s.
      • As k-mers are subsampled, sensitivity in remote homology detection is decreased.
    • --space-mask: Use spaced k-mers instead of contiguous ones.
    • --custom-metamer: Specify k-mer length and customize a translation table.

v1.1.1

  • --validate-input option added for FASTA/Q validation.
  • --validate-db option added for database validation.
  • classifiedRefiner module added to refine classification results.

v1.1.0

  • Fix errors in v1.0.9
  • Custom DB creation became easier
  • Improve updateDB command

v1.0.9

  • DB creation process improved
  • updateDB module to add new sequences to an existing database.
  • Users can provide CDS information to skip Prodigal's gene prediction.
  • --max-ram parameter added to build module.
  • Compatibility with taxdump files generated using taxonkit.

v1.0.8

  • Added extract module to extract reads classified into a certain taxon.

v1.0.7

  • Metabuli became faster 🚀
    • Windows: 8.3 times faster
    • MacOS: 1.7 times faster
    • Linux: 1.3 times faster
    • Test details are in GitHub release note.
  • Fixed a bug in score calculation that could affect classification results.