v0.6.0

[0.6.0] (2 April 2024)

This release of Dorado improves performance for short read basecalling and RBK barcode classification rates, introduces sorted and indexed BAM generation in Dorado aligner and demux, and updates the minimap2 version and default mapping preset. It also adds GPU information to the output BAM or FASTQ and includes several other improvements and bug fixes.

New feature highlights

1. --emit-summary option to generate summary files from dorado demux and dorado aligner.
2. Support for loading inputs from/saving outputs to a folder fordorado demux and dorado aligner
3. --bed-file option in dorado aligner to capture alignments hits in specific intervals of the reference. Hits per read stored in the bh:i tag.
4. --sort-bam option in dorado demux to output sorted reads when input is sorted and barcodes are not trimmed.

Changes to default behavior

1. Default mapping preset for dorado aligner updated to lr:hq.
2. dorado trim and dorado demux now output unaligned records by default (i.e. all alignment information such as tags and headers removed).

Backwards incompatible changes

1. New scoring parameters for barcode classification to support an updated classification algorithm. Older scoring config files will no longer be compatible.

All key changes

• dc22d7f - Update method for barcode classification
• e65eaf4 - Improve basecalling speed on short reads
• f0b829d - Emit sorted, indexed BAM files from dorado demux and dorado aligner
• 913f062 - Add DS:gpu information to output FASTQ and SAM/BAM files
• c459890 - Added support for demux and aligner reading from a folder and a --recursive option
• d994a4d - Add --emit-summary option to dorado demux and dorado aligner
• 246b9b9 - Add --bed-file argument to dorado aligner
• f6b6554 - Add --sort-bam option to dorado demux
• 9b49ae5 - Update to minimap2-2.27 and use lr:hq as default mapping preset
• a0f9462 - Add RG and st tags to FASTQ for consistency with BAM
• ae47155 - Calculate mean Q-score for RNA on bases after the poly(A)
• 3cf15fa - Trimming rapid adapter from raw signal
• b40d001 - Improve read splitting for RBK
• 9d3af87 - Trim low-quality data from reads with end reason mux_change or unblock_mux_change
• ec106d6 - Improve performance of calling modified bases on NVIDIA GPUs
• 77c5599 - Improve Apple silicon auto batch sizing
• b4fdb24 - Fix bug with MM/ML tags not updating correctly with dorado trim
• bacd354 - Remove invalidated tags if running dorado demux or dorado trim on aligned BAM
• b6077db - Fix bug with modbase model auto detection on @v0
• ba0d708 - Ensure ts set to zero if --no-trim or --estimate-poly-a enabled
• 12c5a3e - Fix duplicate SQ lines in header of aligned BAM
• 9dc052d - Ensure read group header lines include custom barcodes
• e8fb085 - Skip barcode trimming when running poly(A) estimation
• bbe6ad6 - Handle issues related to user locale
• bdc05e3 - Fix bug using simplex-only model complex and --modified-bases{-models} arguments
• b31e5c8 - Fix resume loading for split reads
• 2919fe0 - Fix bug with custom barcode arrangements
• 98763da - Fix bug when aligner writing to stdout
• 74b4b53 - Fix regression with calling modified bases on macOS
• 3929003 - Perform an allocation-less matmul when using torch
• 6f283a5 - Prevent CUDA OOM due to small allocations
• 0fa2c2f - Fix Cuda OOM during batch size calculation
• 7506d44 - Add support for additional barcodes
• 13ba5af - Add deprecation warning for FAST5
• b5dc9f8 - Update to Koi v0.4.5
• c9c5ad0 - Update to POD5 v0.2.4
• 901f700 - Improve error reporting when the device string is invalid for CUDA devices
• e3442ec - Log errors reported by Metal and enable warnings
• e61cfe4 - Output Dorado commandline arguments in logs
• de59f33 - Move default download path for third-party libraries into the build folder
• d7defcc - Log a warning message if running on Apple Silicon with less than 16GB RAM
• 8dfd180 - Consolidate pipeline node input thread handling
• 4018823 - Update DEV.md to install the correct package