wf-basecalling (v1.5.0) bundles the dorado basecalling software into the EPI2ME ecosystem.
- The bundled version of Dorado has been updated to v0.9.5 - the dorado changelog contains more information.
- The update also implements a fix so that basecaller metadata is maintained for use in downstream workflows
wf-single-cell (v3.1.0) provides functionality for the analysis of single-cell transcriptomic datasets prepared from 10x Genomics library types.
- This release introduces new experimental support for SNV calling - this can reveal the genetic heterogeneity that is frequently obscured in bulk sequencing and provides crucial insights into cell population architecture, especially in cancer data sets.
- The workflow report has been refreshed and now includes a more detailed experiment summary section.
- Fix has been implemented to prevent excessive memory usage at the expression matrix creation stage.
- Fix for to report supplementary reads that had been missing from the tagged BAM output file.
wf-metagenomics (v2.13.0) and wf-16s (v1.5.0)
- This workflow release provides updates to the included metagenomic source databases:
  - Kraken2 indexes have been synchronised with releases dated 2024-12-28
  - NCBI Taxonomy database updated to the release dated 2025-01-01
- Output files that describe alignment characteristics including reference sequence, depth of coverage, mean sequencing depth and taxonomic assignment are now included when the Minimap2 classifier is used with the optional minimap2_by_reference parameter - these files are written to : alignment_tables/{{ alias }}.alignment-stats.tsv (default: False)
- Any unclassified sequences from either Minimap2 or Kraken2 classifications can now be output to FASTQ file by specifying the optional output_unclassified parameter (default: False) - this can facilitate further analysis of sequences that cannot be explained by the standard sequence databases.
- Fix error: an issue leading to a workflow error when classiying sequences using the SILVA database has been resolved - bracken-build: line 231: syntax error: unexpected end of file
- Fix: Reduce disk usage and time when running the antimicrobial resistance gene analysis option.
wf-flu (v1.2.4)
- Fixes an error where single sample runs failed during report generation - this was due to an expectation of a barcode metadata field.
wf-clone-validation (v1.8.0) - our workflow for the analysis of multiplexed plasmid sequencing database has been updated to improve to robustness of assemblies.
- The minimum quality score for a sequence has been parameterised and is now set as 9 by default. Increasing this value may be recommended when there are thousands of sequence reads for each multiplexed sample.
- Trim length, the number of bases clipped from each end of the sequence, is now set to 0 by default. This change simplifies the assembly of shorter plasmids.
- Improvement to post assembly deconcatenation have been introduced.
wf-transcriptomes (v1.7.0) - our workflow for the analysis of direct RNA or cDNA sequence data has introduced a number of fixes.
- The update fixes an issue in the differential expression analysis and exons are now correctly counted.
- A memory fix better handles memory usage during the data reporting process.
- Updated error messages are now returned when mismatched ref_annotation and ref_genome information are provided.

Dataset release - DNA sequence data from collection of 96 multiplexed plasmids has been released to our ont-open-data project. This set of challenging to analyse plasmids contains a variety of sequence duplications, whole plasmid duplications and a variety of other repeat contexts. More information on the dataset can be found with the dataset release blog post.

We welcome any feedback, recommendations for future bioinformatics workflows and would be interested to hear about datasets and blog posts that would be of interest.