ANNEXA v.3.2.0

New features:

• Added Stringtie2 as alternative transcript reconstruction tool (--tx_discovery stringtie2). Bambu is used as default tool.
• Added CDS prediction with TransDecoder. CDS information is added to extended annotations.
• Added gffcompare class codes information in extended annotations
• Updated Bambu to version 3.4.0
• Added ability to keep or discard single exon transcripts (SET) when using Bambu (--bambu_singleexon). SETs are kept by default.
• Added --help information.

Changes:

• Reworked QC pdf.

ANNEXA v3.1.1

• Fix: Downgrade mkl to version 2024.0.0 to prevent issue with PyTorch

ANNEXA v3.1.0

• New feature: strand identification for reads with undefined strand based on transforkmers probability
• New feature: add 'bambu_strand' launch option to indicate to bambu which protocol is used (bambu_strand true for dRNA protocol, bambu_strand false for cDNA protocol, TRUE by default)

ANNEXA v3.0.1

• Patch with README updates
• Usage by default now using singularity (instead of conda)

v3.0.0: Merge pull request #5 from IGDRion/dev

New Annexa release v3.0.0

• Update with new Bambu version ( v2.0.6 to v3.0.8)
  • gn and tx names have changed and columns have been filtered accordingly
• TFK environment has been updated directly on the repo
• Mode intersection (NDR + TFK) should be the default

ANNEXA-2.1.0

This release corrects:

• TFK threshold
• inclusion of lncRNA with noORF
• exclusion of retained intron biotype
• increase memory processes

v2.0.1

First ANNEXA release

• set as v2.0.1

Include in merge

• Change hub.docker to GitHub Packages.
• Fix number exons in QC.
• Retrieve mono-exonic transcripts.