1.6.0

Fieldbioinformatics now supports segmented viruses and amplicon panels.

What's Changed

• Add support for segmented genomes / amplicon panels by @BioWilko in #146

Full Changelog: v1.5.8...v1.6.0

1.5.8

Add Seqtk dependency

Full Changelog: v1.5.7...v1.5.8

1.5.7

Update which adds functionality to pick the most appropriate reference for multi reference primer schemes.

What's Changed

• Add reference selection functionality for multiref schemes (currently only artic-inrb-mpox) by @BioWilko in #147

Full Changelog: v1.5.6...v1.5.7

1.5.6

What's Changed

• 1.5.6 PR (fixes #144) by @BioWilko in #145

Full Changelog: v1.5.5...v1.5.6

1.5.5

What's Changed

• Switch out muscle for mafft by @BioWilko in #143

Full Changelog: v1.5.4...v1.5.5

1.5.4

Remove the platform tag from the docker image build to avoid nextflow image pull issues.

Full Changelog: v1.5.3...v1.5.4

1.5.3

Fix artic --version

Full Changelog: v1.5.2...v1.5.3

1.5.2

Small changes to fix setup.cfg and shrink dockerfiles

Full Changelog: v1.5.1...v1.5.2

1.5.1

ARTIC Fieldbioinformatics v1.5.1

Well hasn't this been a long time coming?

Major Changes:

• Fieldbioinformatics now supports rapid barcoded (fragmented) primer trimming and normalisation
• Nanopolish has been removed completely due to several compatibility issues
• Medaka has also been removed completely due to kicking out long indels in a way that cannot be changed.
• Clair3 is now the default variant caller, by default only the r9.4.1 models are available but a artic_get_models command has been added which will fetch the ONT created r10.4.1 models listed in the rerio repository.
• The pipeline will also attempt to pick an appropriate model based on the basecall_model_version_id field that is added to read headers by default by ONT sequencers.
• Removed longshot entirely, it also kicks out long variants and is now unnecessary due to clair3 being a much better variant caller.
• Primer scheme fetcher has been updated to pull from the quick-lab primal hub schemes repository. For schemes not available in this repository you may provide them directly with the arguments --bed and --ref.
• Automated docker builds pushing to quay.io for use in nextflow pipelines etc.
• Remove some old functionality which is no longer relevant (basecalling, gather, etc)
• Re-implement CI as a gh action.
• Fix the overlapping variants issue by normalising variants against the pre-consensus using bcftools norm.

What's Changed

• Version 1.5.1 Release by @BioWilko in #137

Full Changelog: v1.2.4...v1.5.1

1.2.4

What's Changed

• Update vcftagprimersites.py by @mattloose in #123

New Contributors

• @mattloose made their first contribution in #123

Full Changelog: v1.2.3...v1.2.4