diff --git a/CHANGELOG.md b/CHANGELOG.md index bf8f663fb..589a1d483 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,14 @@ All notable changes to Dorado will be documented in this file. +# [0.4.1] (12 Oct 2023) + +This release of Dorado fixes a bug with duplex tags and adds functionality to dorado demux. + +* 7fefd5d949d32decc3b347778afa80c90b9c6417 - Fix missing `dx:i:-1` tag for simplex reads with duplex offsprings +* d532ef1517413b536714d47c01a998305890d922 - Enable dorado debug build in Visual Studio 22 +* eeef7575b6dabab8d5647cebed0f92ef793786ef - Add `dorado demux` option to demux pre-classified barcoded data + # [0.4.0] (9 Oct 2023) This release of Dorado introduces barcode demultiplexing, barcode trimming, simplex read splitting, and updated models for calling 6mA and 5mC/5hmC modified bases. Furthermore, it contains improvements to duplex pairing for increased yield, basecalling speed enhancements and reductions to memory consumption, bug fixes, and additional tests for enhanced stability. diff --git a/README.md b/README.md index d02eb3f08..992a5a051 100644 --- a/README.md +++ b/README.md @@ -18,10 +18,10 @@ If you encounter any problems building or running Dorado, please [report an issu ## Installation - - [dorado-0.4.0-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-linux-x64.tar.gz) - - [dorado-0.4.0-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-linux-arm64.tar.gz) - - [dorado-0.4.0-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-osx-arm64.zip) - - [dorado-0.4.0-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.0-win64.zip) + - [dorado-0.4.1-linux-x64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-linux-x64.tar.gz) + - [dorado-0.4.1-linux-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-linux-arm64.tar.gz) + - [dorado-0.4.1-osx-arm64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-osx-arm64.zip) + - [dorado-0.4.1-win64](https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.4.1-win64.zip) ## Platforms @@ -104,7 +104,9 @@ To run Duplex basecalling, run the command: $ dorado duplex dna_r10.4.1_e8.2_400bps_sup@v4.1.0 pod5s/ > duplex.bam ``` -This command will output both simplex and duplex reads. The `dx` tag in the output BAM can be used to distinguish between them: +When using the `duplex` command, two types of DNA sequence results will be produced: 'simplex' and 'duplex'. Any specific position in the DNA which is in a duplex read is also seen in two simplex strands (the template and complement). So, each DNA position which is duplex sequenced will be covered by a minimum of three separate readings in the output. + +The `dx` tag in the BAM record for each read can be used to distinguish between simplex and duplex reads: * `dx:i:1` for duplex reads. * `dx:i:0` for simplex reads which don't have duplex offsprings. * `dx:i:-1` for simplex reads which have duplex offsprings.