v0.8.1

[0.8.1] (03 Oct 2024)

This release of Dorado includes fixes and improvements to the Dorado 0.8.0 release, including corrected configuration for DNA v5 SUP-compatible 5mC_5hmC and 5mCG_5hmCG models, improved cDNA poly(A) tail estimation for data from MinION flow cells, reduced basecaller startup time on supported GPUs, and more.

• f74d891 - Corrected bug causing [email protected]_5mC_5hmC@v2 to call CpG contexts only and [email protected]_5mCG_5hmCG@v2 to call all contexts
• eb46494 - Improve cDNA poly(A) tail estimation for MinION flow cells
• 762e886 - Cache batch sizes to significantly reduce basecaller startup time on supported GPUs
• 22269a8 - Prevent "Trim interval is invalid for sequence" error when performing trimming
• f156ae6 - Prevent write permission error for model download folder when file write is not required
• fcb9d53 - Include run name in output files from dorado demux even if input files are FASTQ
• a4c9649 - BED file handling: only split columns on tabs, not spaces; load files with spaces in region names
• e62cbc8 - Allow comment lines in the middle of the BED file
• f15c0b3 - Fix compilation in AppleClang 16

v0.8.0

[0.8.0] (16 Sept 2024)

This release of Dorado adds v5.1 RNA models with new inosine_m6A and m5C RNA modified base models, updates existing modified base models, improves the speed of v5 SUP basecalling models on A100/H100 GPUs, and enhances the flexibility and stability of dorado correct. It also introduces per-barcode configuration for poly(A) estimation with interrupted tails, adds new --output-dir and --bed-file arguments to Dorado basecalling commands, and includes a variety of other improvements for stability and usability.

• a69c0a2 - Add v5.1.0 RNA basecalling models, including new inosine_m6A and m5C modified base models, and updated existing DNA and RNA modified base models
• 8e3a870 - Improve speed of v5 SUP basecalling models on A100 and H100 GPUs
• 6ee9018 - Reduce false positive calls from v5 DNA modifed base models
• 69cb260 - Fix bug causing intermittent crashing with v5 SUP models
• e9dec49 - Add --resume-from functionality to dorado correct
• cb6eee1 - Decouple alignment and inference stages in dorado correct
• df861db - Prevent segfaults in dorado correct
• f35c8cc - Fix bug when downloading models for dorado correct
• 6646701 - Add per-barcode poly(A) configuration for interrupted tails
• 0b79407 - Improve poly(A) length estimation for RNA and DNA
• df614ab - Add --output-dir argument to dorado basecaller and dorado duplex
• f9beb39 - Add --bed-file argument to dorado basecaller and dorado duplex
• 1fc6f1e - Add --models-directory option to basecaller, duplex, and download to download and reuse models
• 966c2ca - Update POD5 version to v0.3.15
• 6ec77c8 - Fix errors when performing duplex calling with modified bases
• 4a28d58 - Always trim DNA adapter signal before processing RNA reads
• a90fbf9 - Fix loading of FASTQ files containing RNA with U bases
• 9e5db84 - Fix duplicated alignment tags in re-aligned files
• 3cc4de3 - Prevent "Too many open files" error when using --sort-bam with dorado demux
• b531918 - Prevent dorado basecaller crash when signal-space trimming removes all raw data
• adc60ba - Package libcupti.so into ARM Linux builds
• 667d160 - Remove kit name requirement in custom barcode configuration
• e9281fa - Emit an error message if header from input HTS file cannot be read
• 7f42b8f - Warn and exit instead of crashing if a model path does not exist
• 7d74246 - Improve index file error handling
• c77733a - Add a mechanism to cache auto batch size calculations
• a674dad - Update --help documentation for basecaller, duplex, and correct
• 022901e - Fix JSON output when using --list-structured with dorado download
• db73e5d - Add run_id to filenames output by demux

v0.7.3

[0.7.3] (1 Aug 2024)

This release of Dorado updates dorado correct to fix handling of high copy repeats and avoid shutdown hanging. It also includes dorado demux improvements to reduce false matches in midstrand barcode detection and ensure correct file naming, along with other fixes.

• 5dc78ab - Remove limit on number of overlaps considered during all-vs-all alignment in dorado correct
• 2741de7 - Prevent hang during shutdown of dorado correct and prevent out of memory errors
• 37d316c - Remove unused --read-ids and --threads parameters from dorado correct
• ddb13de - Increase the threshold for midstrand barcode detection to reduce false matches
• 845a3ad - Fix misnaming by dorado demux of barcode file for barcodes ending in a letter (e.g., 12a)
• 56d3e8e - Fix seq/qual orientation when demultiplexing aligned BAMs
• 5ddfc2f - Fix bug causing CUDA illegal memory access with v5 RNA SUP and mods

v0.6.3

[0.6.3] (31 July 2024)

This release matches the version of Dorado in MinKNOW 24.06 and Dorado Basecall Server 7.4.12.

• 29f311b - Increase the threshold for midstrand barcode detection to reduce false matches
• 01735dd - Fix misnaming by dorado demux of barcode file for barcodes ending in a letter (e.g., 12a)
• c65f1f3 - Fixes to support live basecalling in MinKNOW

v0.7.2

[0.7.2] (18 June 2024)

This release of Dorado resolves basecalling failures when running v5 SUP models on CPU-only devices or v5 RNA HAC on Apple silicon. It also fixes bugs in dorado demux and dorado correct, and corrects sm and sd tags to match the Dorado SAM specification.

• 3835272 - Fix bug causing v5 SUP models to fail when running on CPU-only devices
• c36f444 - Fix bug causing RNA v5 HAC basecalling to fail on Apple silicon
• 3621800 - Fix bug causing segfault in dorado demux
• 3b51c1b - Fix sub-par alignments in dorado correct
• d0df79c - Correct shift and scale (sm and sd) SAM tags to match SAM specification

v0.7.1

[0.7.1] (3 June 2024)

This release of Dorado fixes out of memory errors when using the v5 SUP model with methylation calling, resolves several bugs in dorado correct and adds correct handling of the BC:Z tag when running demux multiple times.

• a9c6f59 - Fetch available memory correctly for autobatch calculation with modbase models
• eb24124 - Move developer quickstart and extend installation instructions
• 45b8acc - Package missing CUDA Toolkit dependencies with dorado
• 33578e7 - Update BC tag instead of adding a new one
• 580ad61 - Prevent creation of CUDA stream when device is CPU
• 82078c5 - Fix segfault with htslib pointer freeing in Windows

v0.7.0

[0.7.0] (21 May 2024)

This release of Dorado introduces new and more accurate v5 models for improved basecalling. It also adds a new subcommand, dorado correct, for single-read error correction to help Nanopore based de novo assemblies of haploid or diploid genomes. In addition, this release contains a slew of bug fixes, stability enhancements and updates to barcode classification.

New feature highlights

1. DNA, RNA and duplex basecalling models with improved single read accuracy.
2. Support for 4mC_5mC methylation calling in DNA and all-context m6A and pseU in RNA.
3. dorado correct subcommand for single-read error correction of haploid and diploid genomes (for assembly pipelines).
4. Poly(A) tail estimation for plasmids and transcripts with interrupted tails.
5. Support for --junc-bed minimap2 splice option.
6. Faster BAM indexing and sorting code.

Changes to default behavior

1. Data type of mean Q-score tag (qs) updated to float.
2. Adapter trimming is enabled when poly(A) estimation is requested.

All key changes

• 7a09ca3 - Add v5 basecalling models for DNA, RNA and duplex
• 159b73c - Add new models for calling DNA and RNA base modifications (4mC_5mC, m6A, pseU)
• be8ac08 - Add dorado correct support for read error correction
• 67dc5ba - Poly(A) estimation for plasmids and interrupted tails
• 381f6c3 - Enable adapter trimming when poly(A) estimation is requested
• d6b0f68 - Change data type of mean Q-score (qs tag) to float
• f938c41 - List supported models in structured format
• 70ff95d - Enable dorado summary to run on trimmed BAM files
• 6373792 - Detect presence of midstrand barcodes to reduce false positive classifications
• 68d40da - Add support for --junc-bed minimap2 splice option
• c443f75 - Output BAM instead of SAM from dorado trim command
• a3dce7e - Support dorado demux from input folders with mix of PG and SQ headers
• 08e2c7b - Speed up sorting and merging of BAM files
• b8de2d9 - Set maximum memory sizes in minimap2
• b8de2d9 - Calculate scaling for RNA on non-adapter signal only
• c88e9f7 - Update CMake Minimum Version to 3.23

v0.6.2

[0.6.2] (9 May 2024)

This release of Dorado disables trimming of the rapid adapter during basecalling which was causing some RBK datasets to have a high unclassified rate during demux.

• a64492b - Fix bug with loading reverse aligned records in dorado demux and trim
• 6cc278f - Disable rapid adapter trimming to prevent signal overtrimming in some RBK datasets

v0.6.1

[0.6.1] (23 April 2024)

This release of Dorado fixes bugs in dorado aligner related to using presets incorrectly and in dorado demux which were causing demultiplexed outputs to be malformed.

• 3e060db - Skip stripping of SQ header lines in dorado demux --no-classify
• a2abf83 - Fix incorrect overriding of minimap2 options when minimap2 preset is specified
• 1cc207a - Fix bug causing unclassified records from dorado demux to be unreadable by samtools
• 2982771 - Fix issue with allocating memory on unused GPU during basecalling
• fa79f4a - Fix reverse strand alignments when re-mapping a SAM/BAM file with dorado aligner
• 3b2c825 - Propagate sv tag to split reads
• 11675a5 - Fix bug where errors were being swallowed in HtsFile class
• 73046e1 - Fix typo in Warnings.cmake

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