Changelog updates

CHANGELOG.md

@@ -4,46 +4,39 @@ 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.
+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.
-3. PolyA tail estimation for plasmids and transcripts with interrupted tails.
-4. `dorado correct` subcommand for single-read error correction of diploid genomes (for assembly pipelines).
-5. Support for --junc-bed mm2 splice option.
+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 PolyA estimation is requested.
+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)
-* cf46f49c620633bf724904b834e8d394073d0bc4 - Raise error if PolyA config file is not found
-* dc50b97605762423d09d91ec74dd95ad2b5c97c9 - Add MacOS support for v5 basecalling model
+* 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
-* 7a09ca3d1d1e469570a7df1e5819c39e9dd2325e - Add v5 models for DNA, RNA and duplex
 * 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 mm2 splice option
-* 93632025d7df195be625654d968f62321c4a4136 - Update barcode kit names
-* 381f6c3038fb69523ea591b1942d3293d7e9b9aa - Enable adapter trimming when polyA estimation is requested
-* be8ac08652d5fe0b73c1126048b7fd96f29f3419 - Add `dorado correct` support for read error correction
-* a30c489c41bafb3e307060806c5b57caa2c610ef - Use new transformer Koi fused residual rmsnorm kernel
-* c443f75314708b7aed0aafa38fffdb8b2e76e9f2 - Output BAM from dorado trim command
-* eaf4ab28d958c4426a6f57eb9c2a7032d5e1fa80 - Update documentation to reflect new `dorado aligner` defaults
-* a3dce7ebe298ce3e17f3d61ad180b099700afb6a - Demux header merge improvements
-* 67dc5bab58d74ee636e492619a6802db38059534 - Plasmid polyA estimation
-* 6ccf0ed46d275c1e0209de3cb99d0bd56bf7f083 - Add support for v5 basecalling model
-* 08e2c7bb2538c2ba89203a68bbf153e6a6054535 - Index BAM while merging temp files
-* b8de2d900d9aeb1c349931a216db7e05aa2ff2c4 - Set max memory sizes in minimap2
-* b8de2d900d9aeb1c349931a216db7e05aa2ff2c4 - Calculate scaling for rna on non-adapter signal only
-* 949d13ffb41152aaba4df9004d01e8584c8038e3 - Write multiple temp files for sorted bam output
+* 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)