bio-workflows-outbreak-pipeline

Prerequisites

conda install -c bioconda mlst abricate snippy iqtree fasttree

pip install treetime transphylo biopython pandas matplotlib

## Step 1a: MLST Typing (Parallel)

```bash
#!/bin/bash
ISOLATES="isolate1.fasta isolate2.fasta isolate3.fasta"
OUTDIR="outbreak_results"
mkdir -p ${OUTDIR}/{mlst,amr,alignment,phylo,transmission}

## Run MLST on all isolates

echo "=== MLST Typing ==="
for fasta in $ISOLATES; do
    sample=$(basename $fasta .fasta)
    mlst $fasta > ${OUTDIR}/mlst/${sample}.mlst.txt
done