Tags: dominikstanojevic/tombo
Tags
Version 1.5 release. This release includes two major feature addition… …s. The first is motif-specific model (packaged with CpG, dam and dcm models) which provide more accurate detection of modifications in known contexts (available via the command). The second feature is level sample comparison which allows for more sensetive modified base detection in certain experiments, especially direct RNA experiments with a control sample (available via the command). This release also fixes a design flaw in the per-read statistics output, especially effecting high coverage samples (fixes nanoporetech#114, fixes nanoporetech#115). Other minor bug fixes and optimizations included as well.
Version 1.4 release. This release includes major improvements to RNA … …signal processing (via resquiggle command), a major re-write of the Tombo python API, and use of the canonical model as a prior for control sample comparison modified base detection. The RNA updates fix a number of github issues (Thank you for all user reports! fixes nanoporetech#98, fixes nanoporetech#82, fixes nanoporetech#79, fixes nanoporetech#68, fixes nanoporetech#64, fixes nanoporetech#55). The API re-write addresses several github issues (fixes nanoporetech#99, fixes nanoporetech#76; fixes nanoporetech#66, fixes nanoporetech#25). A change in the statistics file format has been resolved (fixes nanoporetech#80). Several other issues resolved as well (fixes nanoporetech#96, fixes nanoporetech#91, fixes nanoporetech#73, fixes nanoporetech#70).
Version 1.3 release. This release includes updates to signal normaliz… …ation procedure (including sequence-dependent iterative re-scaling) and an outlier-robust alternative model comparison method. These updates drastically increase the accuracy of Tombo modified base predictions. Many other computational optimizations and bug fixes. Added 5mC RNA model (fixes nanoporetech#50). Updated RNA model to 180mV model (fixes nanoporetech#63). Increased read filtering capabilities. Re-factored Tombo commands into command groups.
Minor fixes for some python2 bugs. Addressed nanoporetech#42. Fixes n… …anoporetech#41.
Minor fixes for some python2 bugs. Addressed nanoporetech#42. Fixes n… …anoporetech#41.
Major tombo update. Added 6mA alternative model, improved re-squiggle… … via parameter tuning, per-read statistics output including random genomic access API, cleaner UX (python3 compatible, mappy/minimap2 genomic mapping, simplified options) and more. Fixes nanoporetech#24. Addresses issues nanoporetech#23, nanoporetech#22, nanoporetech#21, nanoporetech#19, nanoporetech#17 and nanoporetech#16.
Added pre-processing command to annotate raw FAST5s with basecalled s… …equence from a FASTQ. Also fixed several minor bugs and updated documentation. Added a note to docs for RNA addressing nanoporetech#9. Corrected minor bug in SAM parsing, closes nanoporetech#10. Re-factored Tombo events access code, closes nanoporetech#11 and closes nanoporetech#14. Minor fix to wiggle output function, closes nanoporetech#13. Minor fix to extract genome sequence from reads function, closes nanoporetech#15. Bumped to version 1.1.1
Minor version upgrade to Tombo to version 1.1. This update includes m… …ajor changes to the alternative base model estimation as well as a new default 5mC model trained with this new method. Also added full detailed documentation to the repo. This version addressed issues from nanoporetech#2, nanoporetech#4, nanoporetech#5, nanoporetech#7, nanoporetech#8 and nanoporetech#9.
PreviousNext