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@tijyojwad tijyojwad released this 21 May 17:30
· 71 commits to release-v0.7 since this release
v0.7.0
71cc744

[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
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