Yet Another Nemo Fish

• 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

Another Nemo Fish

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

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

v2.4.1

Add Guppy 6.0.0 support.

v2.4.0

Remora modified base calling

Minor bug fixes also included in release

Nigel

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

Tad

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

Gurgle

Fix bug due to guppy 5.0.7 upgrade. Resolves #146

Sheldon

This patch release includes a number of bug fixes and two new features.

• New features
  • Modified base validation from taiyaki mapped signal (basecaller training) file
    • Allows easier validation of model performance and assessment of overfitting
  • Command line access to minimap2 scoring parameters
• Bug fixes
  • Live processing fixed
  • mapping.summary.txt docs ( #145 )
  • Better handling of corrupt FAST5 files

Bloat

Fix bug where calibration files were not included in source release. (Resolves #128)

Pearl

This minor release implements upgrades to the guppy interface.

• Guppy interface upgrades
  • Convert from batching to streaming
  • Default calibration files for guppy 4.5.2 modbase models
  • Simplified Guppy logging
• Install upgrades
  • Numpy no longer required before Megalodon install
  • sklearn -> scikit-learn
• Faster HDF5 reading (via driver="core")
• black formatting (https://black.readthedocs.io/en/stable/)
• Various bug fixes