We are pleased to announce wf-transcriptomes v2.0.0, a major refresh of our long-read transcriptomics workflow. This release modernises the workflow around a new reference-guided analysis approach built on bambu, with SQANTI3 for transcript classification and QC, DESeq2 for differential gene expression, DEXSeq for differential transcript usage, and per-sample modified base summarisation with modkit when modification tags are present in aligned BAMs.

The new version is designed to improve robustness, reduce common workflow breakpoints, and provide a clearer and more consistent output structure for transcript discovery, quantification, QC, and downstream analysis.

New release:

wf-transcriptomes v2.0.0

Rebuilt the workflow around bambu for reference-guided transcript discovery and quantification, replacing the previous StringTie / GffCompare / Salmon-based approach.
The primary transcriptome result is now a shared cohort transcriptome built from all samples together.
Added richer per-sample outputs, including transcriptome GTF, FASTA, count tables, transcript metadata, and QC summaries.
Differential gene expression now uses DESeq2.
Differential transcript usage continues to use DEXSeq, now driven from the shared bambu outputs.
Added transcript classification and QC for both cohort and per-sample transcriptomes with SQANTI3.
Improved workflow validation so prerequisites and experimental design issues are caught earlier in the run.
Refreshed the output structure around:
- cohort/
- samples/<alias>/
- de_analysis/<contrast>/
Differential analysis outputs are now organised per contrast under de_analysis/<contrast>/
Added support for two transcriptome modes via --transcriptome_mode:
- discover
- fixed_annotation
Added per-sample modified base summarisation from aligned BAMs with MM and ML tags using modkit, including:
- bedMethyl pileups
- per-sample modification summary tables
- per-modification bigWig tracks
Refreshed the report with new visual components, including:
- sample-level hierarchical clustering
- PCA plots
- distance heatmaps
- contrast-level interactive volcano plots