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agat_sp_manage_IDs.pl silently drops child records when renamed level-2 IDs collide with pre-existing hash keys

Status: Open.

#597 In NBISweden/AGAT;

· WimSpee opened on Jul 14, 2026

Adding GO:terms and Reactome:terms to gff3 using agat_sp_manage_functional_annotation.pl from InterproScan-V6

Status: Open.

#595 In NBISweden/AGAT;

· desmodus1984 opened on May 15, 2026

agat_sp_manage_functional_annotation.pl

Status: Open.

#594 In NBISweden/AGAT;

· okendojo opened on May 15, 2026

AGAT v1.7 causing issues with table2asn, unexpectedly changing feature IDs

Status: Open.

#593 In NBISweden/AGAT;

· rhiannon-schembri opened on May 8, 2026

Hypothetical proteins

Status: Open.

#592 In NBISweden/AGAT;

· jaredbernard opened on May 6, 2026

Support feature-only filtering while keeping all attributes by default

Status: Open.

#590 In NBISweden/AGAT;

· XiaohuiZhang98 opened on Apr 13, 2026

agat_convert_mfannot2gff.pl defines rns as mRNA instead of rRNA

Status: Open.

#582 In NBISweden/AGAT;

· RilRis opened on Feb 24, 2026

stdout and -f option in agat_sp_fix_cds_phases.pl

Status: Open.

#580 In NBISweden/AGAT;

· dariober opened on Jan 26, 2026

AGAT does not propagate DIAMOND functional annotations to BRAKER GFF3

Status: Open.

#576 In NBISweden/AGAT;

· scaliwalker opened on Dec 19, 2025

Potential problem when extracting sequences

Status: Open.

#568 In NBISweden/AGAT;

· filonico opened on Nov 20, 2025

agat_sp_extract_sequences.pl different gffread

Status: Open.

#566 In NBISweden/AGAT;

· WWz33 opened on Oct 26, 2025

longest exon per gene above a threshold length

Status: Open.

#565 In NBISweden/AGAT;

· bioinfowheat opened on Oct 20, 2025