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v1.3.0 - New Feature: Enhanced Gene Presence/Absence Output for Reclustering

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@NickJD NickJD released this 03 Oct 09:07
· 19 commits to main since this release
v1.3.0
196cc0b

New Feature: Enhanced Gene Presence/Absence Output for Reclustering
Reclustering now generates a gene presence/absence (GPA) file that tracks gene family evolution
When running PyamilySeq with reclustering enabled, the output GPA file now includes:

  • Original gene groups (group_) - Clusters from the initial clustering step
  • Combined gene groups (combined_group_) - Original clusters extended with new sequences from reclustering
  • Second-only gene groups (Second_group_) - Entirely new clusters formed exclusively from reclustered sequences

All gene groups are globally sorted by genome prevalence, allowing users to easily:

  • Identify which original clusters were extended with additional sequences
  • Track how core/accessory classifications changed after reclustering
  • Identify novel gene families that were missed in the initial clustering
  • Compare clustering results before and after adding new sequences

File format: The updated GPA file maintains compatibility with existing Roary/Panaroo downstream analysis tools (Coinfinder) while providing clearer labelling of cluster origins (group_, combined_group_, Second_group_ prefixes).
This enhancement improves transparency in understanding how reclustering impacts pangenome composition and gene family assignments.

Full Changelog: v1.1.2...v1.3.0

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