diff --git a/CHANGELOG.md b/CHANGELOG.md index e78c1a43..240a582c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,63 @@ All notable changes to Dorado will be documented in this file. +# [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 + +* 7a09ca3d1d1e469570a7df1e5819c39e9dd2325e - Add v5 basecalling models for DNA, RNA and duplex +* 159b73c7fea64d374b562af32abeaa382af54354 - Add new models for calling DNA and RNA base modifications (4mC_5mC, m6A, pseU) +* be8ac08652d5fe0b73c1126048b7fd96f29f3419 - Add `dorado correct` support for read error correction +* 67dc5bab58d74ee636e492619a6802db38059534 - Poly(A) estimation for plasmids and interrupted tails +* 381f6c3038fb69523ea591b1942d3293d7e9b9aa - Enable adapter trimming when poly(A) estimation is requested +* d6b0f68b3617f34a321db676b780e1a1183b6060 - Change data type of mean Q-score (`qs` tag) to float +* f938c415ddc9f458fe718af72c82001448d9c3c7 - List supported models in structured format +* 70ff95d84b316adb4701f7f43a19151e73b58b5b - Enable `dorado summary` to run on trimmed BAM files +* 6373792b686538758a16aacb063434c2b3260077 - Detect presence of midstrand barcodes to reduce false positive classifications +* 68d40da45da886384508173219a9fb677fc50cef - Add support for `--junc-bed` minimap2 splice option +* c443f75314708b7aed0aafa38fffdb8b2e76e9f2 - Output BAM instead of SAM from `dorado trim` command +* a3dce7ebe298ce3e17f3d61ad180b099700afb6a - Support `dorado demux` from input folders with mix of PG and SQ headers +* 08e2c7bb2538c2ba89203a68bbf153e6a6054535 - Speed up sorting and merging of BAM files +* b8de2d900d9aeb1c349931a216db7e05aa2ff2c4 - Set maximum memory sizes in minimap2 +* b8de2d900d9aeb1c349931a216db7e05aa2ff2c4 - Calculate scaling for RNA on non-adapter signal only +* c88e9f753219f3c462c3678ddfad6b4561830f33 - Update CMake Minimum Version to 3.23 + +# [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. + +* a64492b69eb59c1d60d602fee1670085338450c4 - Fix bug with loading reverse aligned records in dorado demux and trim +* 6cc278f4d7759a7aaaa9a9b336d843b127b0d7ed - Disable rapid adapter trimming to prevent signal overtrimming in some RBK datasets + +# [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. + +* 3e060db5a35ab09fecbeef9754cc545ba400edf1 - Skip stripping of SQ header lines in dorado demux --no-classify +* a2abf83852e895b1016c690769b59c06587684fe - Fix incorrect overriding of minimap2 options when minimap2 preset is specified +* 1cc207a166b1cafcbd012f5c70b5c817c788c7f3 - Fix bug causing unclassified records from `dorado demux` to be unreadable by samtools +* 298277150ad2522ca6c1928c4981782ce2893a5a - Fix issue with allocating memory on unused GPU during basecalling +* fa79f4a77fca737704d8a9e08d0495b9988f88ef - Fix reverse strand alignments when re-mapping a SAM/BAM file with `dorado aligner` +* 3b2c8252d1a40bb0f941ca2ceca0849be15d15fa - Propagate `sv` tag to split reads +* 11675a565da9af52de89a3f6614d15e57d10765d - Fix bug where errors were being swallowed in HtsFile class +* 73046e19fd443dfb48f3fbb82c0b37c5c7cfb8d5 - Fix typo in Warnings.cmake + # [0.6.0] (1 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. diff --git a/README.md b/README.md index 28084768..b5311c64 100644 --- a/README.md +++ b/README.md @@ -20,10 +20,10 @@ If you encounter any problems building or running Dorado, please [report an issu ## Installation - - [dorado-0.6.0-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-linux-x64.tar.gz) - - [dorado-0.6.0-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-linux-arm64.tar.gz) - - [dorado-0.6.0-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-osx-arm64.zip) - - [dorado-0.6.0-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.6.0-win64.zip) + - [dorado-0.7.0-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.0-linux-x64.tar.gz) + - [dorado-0.7.0-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.0-linux-arm64.tar.gz) + - [dorado-0.7.0-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.0-osx-arm64.zip) + - [dorado-0.7.0-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.0-win64.zip) ## Platforms diff --git a/cmake/DoradoVersion.cmake b/cmake/DoradoVersion.cmake index 92a8c968..8afd63d0 100644 --- a/cmake/DoradoVersion.cmake +++ b/cmake/DoradoVersion.cmake @@ -1,5 +1,5 @@ set(DORADO_VERSION_MAJOR 0) -set(DORADO_VERSION_MINOR 6) +set(DORADO_VERSION_MINOR 7) set(DORADO_VERSION_REV 0) find_package(Git QUIET)