2023.1.1 Bug fix

A small release, with a bug fix.

For major new features introduced in refactored readfish, please see https://github.com/LooseLab/readfish/releases/tag/2023.1.0.

Bug fixes

• Fixes a bug caught by @jamesemery in #289, where regions were required to be present in a TOML file, even when the intent was to use barcoding only.

Other changes

• Adds a Changelog, found in the docs and at the bottom of the README.
• Minor documentation fixes to broken links and problems installing grpcio on Apple Silicon.

2023.1.0 Stable refactored readfish for all platforms

Major Changes

1. This release is a complete overhaul of the inner workings of readfish. Fundamentally nothing has changed in the way readfish works, but we have dramatically improved the compatibility with nanopore platforms, as well as supporting more compute systems including Apple Silicon.

2. This release is compatible with all flavours of PromethION from the lonely p2solo to the gregarious P48. To do this we include a new rust based wrapper for minimap2 which enables multi-threaded mapping. The release also supports GridION and MinION. It is untested on mk1c and we don't recommend using it.

3. This release is compatible with both guppy and dorado via the ont-pyguppy-client-lib and so introduces native support for apple silicon.

4. We also introduce a new readfish stats module which will summarise an experiment given the TOML configuration for readfish and the path to the FASTQs from the run.

5. The code includes all new documentation - see https://looselab.github.io/readfish - and will prevent users from making many common mistakes.

Note

Important: The TOML file specification has been modified for this version and users should update their TOML files accordingly.

This includes a description of the new plugin framework, developed by @alexomics , which will enable users to develop their own custom mappers, squiggle analysis packages and other tools and then integrate them into a common readfish environment.

In principle readfish can be used as a library by other packages.

Full information on new features can be found in the readme and associated documentation. All issues should be reported by the GitHub issue tracker and not by email to the authors.

What's Changed

• Add unblock all script by @alexomics
• Add github worklflow action to close stale issues by @Adoni5
• Move logger initialisation into check that we have arguments by @Adoni5
• Add pre commit and make all files compliant by @Adoni5
• validation script by @alexomics
• Switching behaviour of validate by @mattloose
• Add readfish identifier to appear in guppy server logs by @mattloose
• Feature/describe plugin by @Adoni5
• Remove --chunk-log option by @alexomics
• Implement runsafe and additional logging. by @mattloose
• Implementing check on basecalling model in guppy plugin. This will va… by @mattloose
• Fixes to describe by @Adoni5
• Update _config.py to check barcodes if regions and barcodes are present. by @Adoni5
• Enabling changes to the log for the readuntil client by tools which u… by @mattloose
• Add readfish[mappy,guppy] as default install target by @Adoni5
• Split mappy plugins by @alexomics
• Feature/summarise-entry-point by @Adoni5
• Fix-stats-macos-aarch-test by @Adoni5
• Adding a check for the current break_reads_seconds value and testing … by @mattloose
• Feature/logging-stats-padding by @Adoni5

No take backsies (for real)

BossRuns/V0.0.2

This version of ReadFish contains the updated BossRuns code in response to reviewer comments. ReadFish BossRuns should now be compatible with minknow-core <=5.1.4 and >= 5.0.0 and Guppy >= 6.0.0. The command to run readfish bossruns remains the same, however the guppy address and port are now most likely ipc:///tmp/guppy and 5555.

BossRuns Publication

This release ran with MinKNOW 21.11.7 and MinKNOW Core 4.5.4 and ONT-Guppy 5.1.13.

Nature Biotech paper code archive

This release archives the code used in the Nature Biotech readfish paper.

Important

The README contains instructions on running this set of code, however many of the tools at the given versions, such as ont-pyguppy-client-lib will no longer work with modern MinKNOW. We recommend you use the most up to date readfish, found here https://github.com/LooseLab/readfish/.