v0.9.9

• Add consensus sequences with ability to adjust allele frequencies at which consensus base is represented as IUPAC
• Include taxonomic classification by Kraken2 and Bracken before and after dehosting (pathogen inclusion)
• Generate html file to report results
• Update packages in conda env
• Adjust SNP positions in reference sequence to be relative to user-specified genomic features (GFF3)
• Plot SNP position and frequency according to genes (overlapping and strand-aware)
• Improve documentation
• Add provenance tracking
• Update apptainer containers & conda envs
• Include test profile with test dataset and example report output
• Filter and remove failed samples from downstream results using filter_qc.py based on QC thresholds in nextflow.config and summarize QC + mutation detection results (amplicon pass/fail, SNP visualization, etc.) in an html report with report_results.py.