Notable changes to pangene:
-
Improvement: more aggressive pseudogene filtering. This helps the great ape
graph. -
New feature: added option -E to filter out genes aligned with a single exon
in all input genomes. Graphs constructed from multi-exon genes are usually
cleaner.
Notable changes to pangene.js:
-
Improvement (call): a new bubble finding algorithm via local graph
traversal. Added a filter to remove falsely idenrified bubbles. -
New feature (call): output names of assemblies that support each allele.
-
New feature: added the getaa subcommand to parse Ensembl and GenCode
annotations.
(22 February 2024, r231)