.. _releaseNotes: Release Notes =============================== v4.2.1 ----------------- * Added new ``DNAscent meIODy`` executable which determines inter-origin distance from DNAscent data. * This new executable is compatible with both v3 and v4 detection/forkSense outputs, and hence is backcompatible with data produced on R9.4.1 flow cells. * Data to test ``DNAscent meIODy`` was provided by `Mathew Jones `_, `Subash Rai `_, and `David Cullen `_ at the University of Queensland. We would like to thank them again for being very supportive of the software and the community. * The minimum read length of ``DNAscent detect`` was relaxed from 1000 bp to 100 bp, as this was a frequently requested feature from users. We still advise caution when using DNAscent on very short reads, as it was designed from the ground up with long reads in mind. v4.1.1 ----------------- * Added new ``DNAscent seeBreaks`` executable which determines whether DNA breaks at replication forks. * This new executable is compatible with both v3 and v4 detection/forkSense outputs, and hence is backcompatible with data produced on R9.4.1 flow cells. * Data to test this release was provided by `Mathew Jones `_, `Subash Rai `_, and `David Cullen `_ at the University of Queensland. We are always grateful for their long-term collaboration and we are particularly grateful to them for supporting the release of the software to the community ahead of publication. v4.0.3 ----------------- * DNAscent is now fully compatible with Dorado and POD5. These are now recommended over Guppy and FAST5. * DNAscent outputs BrdU and EdU calls in modbam format. This is now recommended over the previous human-readable table of BrdU and EdU probabilities. * The workflow and visualisation pages of the documentation have been revamped to show how to use these changes. * Guppy, FAST5, and human-readable detection outputs are all still supported to avoid breaking users' previous workflows. * The modbam MM tag for EdU and BrdU specifies ``N+e?`` and ``N+b?``, respectively. Users familiar with the SAM optional fields specification will notice that these are actually the one-letter codes for 5fU and 5caU. We have done this as a temporary measure so that BrdU and EdU can be easily shaded and viewed in IGV (View --> Preferences --> Base Mods). We will replace these one-letter codes with the ChEBI IDs for BrdU and EdU as soon as this is supported by IGV. v4.0.2 ----------------- * The deep learning model is the same as in v4.0.1. Users should see nearly identical performance in BrdU and EdU calling. * Fork speed and stall calling has been fine-tuned from v4.0.1. Users should now see a closer match between v4.0.2 on R10 pores and that of v3.1.2 on R9 pores. * Starting with this release, we will be providing supported Singularity images here (https://cloud.sylabs.io/library/mboemo). This is now the recommended way to use and run DNAscent. * There was a longstanding issue of different basecallers producing slightly different sequencing summary formats which could trip up ``DNAscent index``. Previously, we provided various flags for ``DNAscent index`` to account for the different formats but this was more complicated than it needed to be. ``DNAscent index`` will now tune itself for whatever sequencing summary format you have. * v4.0.1 had an issue where one of the model layers was not properly optimised for GPU usage by TensorFlow 2.12.0. This was causing slow runtimes of ``DNAscent detect`` on certain GPUs. The issue is fixed in this release, although it required a rollback to TensorFlow 2.4.1 (at least for now). Part of our aim in releasing and supporting Singularity images was to mitigate any inconvenience that might have been caused by the need to change CUDA and CuDNN versions. * POD5 and Dorado support are still ongoing. While we missed our target for including them in this release, positive community feedback on v4.0.1 and deprecation of R9 flowcells meant that we wanted to move R10 support out of the pre-release stage and ship a fully supported release to address the above issues. Engineering on quality-of-life features remains ongoing. v4.0.1 ----------------- This is a pre-release. It is possible (maybe even probable) that the deep learning model and other parts of the software will be re-tuned in the coming weeks as we listen to community feedback. * All DNAscent executables now work on Oxford Nanopore R10.4.1 pores. ``DNAscent detect`` detects the thymidine analogues BrdU and EdU in single molecules as in v3.0.2 and v3.1.2. * POD5 is not yet supported but POD5 support is planned for v4.0.2 which will be the LTS release. POD5 can be converted to FAST5 using the ``pod5 convert to_fast5`` utility (https://pypi.org/project/pod5/#pod5-convert-to_fast5). * DNAscent's deep learning models were trained on R10.4.1 flow cells with 5kHz sampling which is now the default sampling rate on Oxford Nanopore platforms. Using DNAscent with reads sequenced with the older 4kHz sampling rate is not recommended. * ``DNAscent index`` still uses the sequencing_summary.txt file from Guppy and legacy versions of Guppy are available on the Oxford Nanopore Community webpage. Compatibility with Dorado is planned for v4.0.2 LTS. * TensorFlow updated to 2.12.0 and, correspondingly, GPU usage now requires CUDA 11.8 and cuDNN 8.9. * Useage is otherwise identical to v3.1.2. * Training data for this release was provided by Mathew Jones at the University of Queensland. This software was developed in collaboration with the `Jones Lab `_, `Merrick Lab `_, and `McClelland Lab `_ to whom we are grateful for their collaboration and support. We are particularly grateful to them for supporting the release of the software to the community ahead of publication. v3.1.2 ----------------- * ``DNAscent forkSense`` now assigns a stall score to each called fork, * ``DNAscent forkSense`` can assign a replication stress signature to each called fork, * ``DNAscent detect`` no longer outputs the reference 6mer corresponding to each thymidine position in order to reduce output file size, * improvements to fork calling and segmentation, * Released with `Jones MJK, Rai SK, Pfuderer PL, Bonfim-Melo A, Pagan JK, Clarke PR, McClelland SE, Boemo MA. A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells. bioRxiv `_. v3.0.2 ----------------- * ``DNAscent detect`` now detects two different thymidine analogues, BrdU and EdU, in the same molecule, * ``DNAscent forkSense`` now uses the spatial patterning of EdU and BrdU to determine fork direction as in DNA fibre, * dnascent2bedgraph utility updated to plot both EdU and BrdU tracks in genome browsers, * ``DNAscent regions`` is now deprecated and has been fully superceded by ``DNAscent forkSense``, * ``DNAscent psl`` is now deprecated as reads can be more comprehensively plotted using the dnascent2bedgraph utility, * Migration from TensorFlow 1.14 to 2.4.1 and, correspondingly, GPU usage now requires CUDA 11 and cuDNN 8, * Released with `Totanes FIG, Gockel J, Chapman SE, Bartfai R, Boemo MA, Merrick CJ. Replication origin mapping in the malaria parasite Plasmodium falciparum. bioRxiv `_. v2.0.0 ----------------- * Migration from HMM-based BrdU detection at every thymidine to ResNet-based detection at every thymidine, * Significant increases to BrdU detection accuracy, * Support for BrdU detection on GPUs, * ``DNAscent forkSense`` to call replication origins and termination sites in both synchronously and asynchronously replicating cells at any point in S-phase, * ``DNAscent align`` to align nanopore signals to reference, * Significant increases to replication origin calling accuracy, * Visualisation utility for plotting output of multiple DNAscent executables as bedgraphs, * Released with `Boemo, MA. DNAscent v2: Detecting replication forks in nanopore sequencing data with deep learning. BMC Genomics 2021;22:430 `_. v1.0.0 ----------------- * HMM-based BrdU detection at every thymidine, * Improvements to BrdU detection accuracy, * ``DNAscent train`` to train Guassian mixture models from nanopolish eventalign. v0.1 ----------------- * HMM-based BrdU detection at ~160 thymidine-containing 6mers, * Assignment of high- and low-BrdU regions based on Z-score, * Replication origin calling for early S-phase cells, * Released with `Muller and Boemo, et al. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nature Methods 2019;16:429-436 `_.