Releases: nanoporetech/megalodon
Squirt
This a point release including new features:
- Allow supplementary alignments with
--allow-supplementary-alignments
flag (resolves #71) - Patch for guppy connection issues (full fix coming with future Guppy release)
- Better Guppy warnings and help pointers
- Add
megalodon_extras calibrate generate_modified_base_stats
command - Lower aggregation batch size default (resolves #76)
Bug Fixes: - describe_alphabet error (resolves #87)
- atomize_variants error (resolves #82)
Ray
Add calibration files for updated 5hmC model as well as megalodon_extras
commands to assist in model training.
Fish School
Fix paths to 5mC model calibration files.
Peach
This a point release including new features:
- Add 5mC Rerio Model calibration files
- Add mapping trimming to summary file
- Optimized modified base aggregation
Bubbles
This point release includes some minor bug fixes and adds minor features and optimizations.
New features:
- Remove requirement for
per_read_mods
output when requestingmod_mappings
- Add script to output all motif hits to a BED file
- Optimize per-site threshold command (for training modified base models)
- Optimize standalone aggregation script when passing valid read IDs
Bug Fixes:
- Fix bug in per-site threshold
signal_mapping
output
Crush
This point release includes some minor bug fixes and adds minor features.
New features:
- New bedmethyl features (
megalodon_extras merge aggregated_modified_bases
) - Expit-scaled modified base aggregation (potentially useful for 5hmC Rerio model; #47)
- More efficient per-site modified base annotation scripts.
Bug Fixes:
- Fix per-read text output commands (fixes #68)
Marlin
This point release includes some minor bug fixes and adds minor features.
New features:
- Sequence variant calibration files for Rerio modified base models
- Improved documentation
- Add API example script (in
tests
) - Optimize
megalodon_extras calibrate generate_variant_stats
command
Bug fixes:
- Fix signal coordinates in mapping summary file
- Fix alphabet printing bug
Gill
This a point release including a number of bug fixes and a few minor new features.
New features:
- Include raw signal endpoints in reference mapping summary file
- Add check for compatible Guppy and pyguppy versions
- Minor improvements to
megalodon_extra validate results
command
Bug fixes:
- Incorrect handling of
mod_mappings
output withsignal_mapping
options (Fixes #58) - Fix error when no modified base scores are added to database
- Fix multiprocessing queues to correctly indicate full output queues
- Fix potential bottleneck for modified base data storage
Dori
This release adds per-site modified base ground truth aided basecaller training data set creation. See docs.
This release also fixes a number of bugs:
Chum
This release includes two internal features to produce more robust processing speeds.
-
Read batching
- Each worker process sends a batch of reads (default 50) to the Guppy basecall server while processing results as they are returned to the client.
- This should enable the Guppy basecall server to process reads more efficiently
-
Signal extraction threading
- Extract read IDs and raw signal using multiple threads (default 8).
- This makes signal extraction more efficient on slower disk or when analyzing single read FAST5 format data.