Megalodon

Latest version: v2.5.0

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2.5.0

* Remora 1.0 support (improved modified base calling for R10.4 E8.1 SUP model; further model support to come in later remora releases)
* Guppy 6.0.6 support

2.4.2

This release includes a number of small bug fixes and enhancements:

- Better handling for Guppy 6 server settings
- Better handling of Remora models

2.4.1

Add Guppy 6.0.0 support.

2.4.0

Remora modified base calling

Minor bug fixes also included in release

2.3.5

This release provides a number of bug fixes and a number of new features.

New features:

- Core methods for constrained basecalling (given constraints on the sequence space; fixed-length and ambiguity codes within sequence)
- Reference-anchored index decoding and basecall-anchored full-path decoding for modified base calling
- Added methods do not significantly effect results. Defaults (unchanged) remain the recommendation
- Partial support for CRF models (cannot run modified base or variant calling outputs)

Bug fixes and optimizations:

- Faster runtimes when not outputting flip-flop modified bases or sequence variant outputs (avoid guppy `--post_out` option)
- Better handling for failed reads from Guppy 5.0+
- Fix bug skipping modified base calls near the ends of reads
- Updates to docs
- Minor bug fixes

2.3.4

This release includes a number of bug fixes and reliability updates.

- Drop python3.5 support
- Better corrupt FAST5 file hanlding
- Fix bug when read id not found in standalone aggregation command
- Handle guppy5 invalid read behavior
- Fix bug in `megalodon_extras validate aggregated_modified_bases` when control sample provided

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