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@iiSeymour iiSeymour released this 16 Sep 21:18
· 93 commits to release-v0.8 since this release
v0.8.0
acec121

[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
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