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1. viral-intrahost-variant-workflowviral-intrahost-variant-workflowPublic

   Containerized Nextflow DSL2 workflow for viral intra-host variant calling (iSNV), quasispecies haplotype reconstruction, and evolutionary selection analysis.

   Python 1

2. rnaseq-nfcore-wrapper-alphavirusrnaseq-nfcore-wrapper-alphavirusPublic

   SLURM execution wrapper and configuration layer for nf-core/rnaseq used in viral RNA-seq projects.

   Python 1

3. libs-spectroscopy-workbenchlibs-spectroscopy-workbenchPublic

   Python software for LIBS spectral processing, baseline correction, elemental line identification, and simulated acquisition.

   Python 12 2

4. preclinical-study-analysis-shinypreclinical-study-analysis-shinyPublic

   R/Shiny app for longitudinal mouse study visualization and export from spreadsheet inputs.

   R

5. lab-bioinfo-templateslab-bioinfo-templatesPublic

   Reusable virology and genomics analysis templates developed for the Jonsson Lab, with a Quarto gallery and synthetic example data.

   R

6. akodon-genome-assembly-workflowakodon-genome-assembly-workflowPublic

   Genome assembly and annotation pipeline for Akodon using 10x Genomics Supernova and BRAKER-based gene prediction on HPC.

   Shell