Note: this document is copied from the repository changelog.
Release notes
v1.4.5: * 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.
v1.1.0-rc1: * Support for read groups: * Support ‘pool’ read groups taken from BED file, e.g.: * nCoV2019_1 * nCoV2019_2 * These can be helpfully viewed in the Tablet viewer. * Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination * Update to nanopolish 0.12.5 fo more informative VCF output * Change nanopore filtering to support new VCF output (e.g. strand-bias) * Support indels with bcftools consensus * Longshot added to Medaka to permit filter VCF on depth * New workflow model - all commands run "one per sample", script nanopolish index * Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather' * Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail * Support for amplicons v3 format file (Will Rowe) * Test suite (Will Rowe) * Documentation (Will Rowe) * Remove old deprecated code (Will Rowe)
v0.13: * ARTIC fork
v0.12: * Update to nanopolish v0.8.4 for Albacore 2.0+ support: * run nanopolish -d /path/to/fast5 input.fasta before zibra.py minion
v0.11-dev: * Add stringent pipeline
v0.11 (25th July 2017): * Revert back to Ryan Wick's porechop repo as --untrimmed now implemented * New script: align_trim_fasta.py and reconstitute.py as basis for more principled demultiplexing (align first, then trim to known amplicon end points +/- 40 bases) to help prevent chimeric reads resulting in incorrect barcode identification
v0.10 (15th July 2017): * Better handling of confident deletions (previously ignored, now N-masked) * Update to nanopolish HEAD * Fixes to support latest nanopolish VCF format changes * Ability to choose higher values of max-haplotypes to support more divergent references
v0.9: * New command line interface zibra.py to ease extraction and demultiplexing with Albacore and multiple groups
v0.8: * Track latest Porechop with better adaptor trimming
v0.7: * Add Illumina wrapper scripts
v0.6: * Update poretools
v0.5: * Update nanopolish to latest HEAD - to fix Albacore 1.1 support (7de633d01cc35a58e5537af5dd1024ae0040d15c) * Add Lassa virus scheme
v0.4: * Update nanopolish to latest HEAD - aaaf90beb4efe37243c651e62fcfd11374fe2176 for Albacore 1 support * Initial support for Yellow Fever (500 and 1000 bp schemes) * Move to poretools for extraction with named basecaller
v0.3: * add Porechop
v0.2: * update nanopolish to 0.6 - adds default support for various nanopore models * update samtools to 1.4