Software downloads

Features:

• Run Until Enhancements: Run Until Coverage and Run Until Barcode Coverage criteria added (Barcode coverage excludes MK1C).
• RNA V5.1 Models: New models support updated m5C and inosine modified bases.
• Poly(A) Tail Estimation: Optional feature to estimate poly(A) tail lengths in RNA sequencing runs.
• Customer Hardware Check – Temperature Monitoring: Temperature measurements conducted across hardware positions with a report produced.

Improvements:

• Data Offload Enhancements: Support for post-run offload , offload to NFS, SMB, and USB locations and offload now include fasta, fasta.fai, and other relevant files.
• Basecalling Defaults: High Accuracy (HAC) basecalling is now the default.
• Firewall Activation: Firewall activation is now enabled with a UI toggle option to switch this on/off. This will block all incoming connections including SSH. Outgoing connections remain possible.
• Run Report Accuracy Metrics: Q Accuracy with Alignment is now visible in the run report.
• Improved UX: Enhanced user experience for handling non-writable locations.
• Post-run Basecalling: Supports running multiple modified base models and defining the Q score filter.
• Pore Occupancy Display: Real-time pore occupancy now visible in the UI.
• Pore Scan Output Filtering: Only complete reads are output during a pore scan.

Bug Fixes:

• Skipped Reads: Improved retry mechanism for basecalling skipped reads.
• Barcoding File Names: Post-run barcoded files now have more specific names.
• Mod Base Selection Fix: Prevents selection of modified base calling when using PCR kits.
• Short Read Filtering: Basecalling now excludes reads <5bp.
• File ID Consistency: BAM and FASTQ files now align using the same protocol_run_id UUID.
• Remote Location Persistence: Temporary remote storage paths now persist after reboot.
• RNA Compatibility Fix: FASTQs from MinKNOW and basecall server are now compatible with standalone barcoding
• Run End Skip Speed: Improved performance during skip stages at end of runs.
• Further Saturation Handling: Additional fixes to saturation on some P2i devices.

Known caveats and additional information:

• Removal of 4 kHz Basecalling Support: In this release, support for 4 kHz basecalling in post-run MinKNOW basecalling has been removed. If you need to process this type of data, please use a legacy version of Dorado.
• POD5 Output Location Bug: When running with Adaptive Sampling or with basecalling disabled, POD5 reads are currently being written to a pod5_skip folder instead of the expected pod5 directory. This issue will be resolved in the next MinKNOW release.
• Firewall & Remote Access Update: Users updating from MinKNOW v24.02 or earlier may experience unexpected remote access blocking due to the introduction of the new firewall feature.