Plasmid_illumina_spades.sh

## Assembly pipeline for Maboni et al. 2022

## Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, 
## Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA

## Pipeline by Isaac Framst (iframst@uoguelph.ca) 
## University of Guelph, Department of Pathobiology
## University of Georgia, Athens Veterinary Diagnostic Laboratory

printf "Run started on $(date) \n"
printf "Hybrid Genomic DNA assembly\n\n"

echo "run ID assignment or isolate name"
read runID

echo "Please specify forward reads file (fastq)"
read fwdRead

echo "Please specify reverse reads file (fastq)"
read revRead

mkdir $runID
cd $runID

metaphlan2 --input_type fastq -t rel_ab_w_read_stats $fwdRead,$revRead,$readsIN_ONT/*.fastq > ${runID}_metaphlan_profile.txt


spades.py -1 $fwdRead -2 $revRead -o ${runID}_spades -m 1024 --plasmid

bwa index ${runID}_spades/scaffolds.fasta
bwa mem -v 2 -M ${runID}_spades/scaffolds.fasta $fwdRead $revRead > bwa_mapping.sam

samtools view -b -S bwa_mapping.sam > bwa_mapping.bam 
samtools sort bwa_mapping.bam bwa_mapping_sorted
samtools index bwa_mapping_sorted.bam

pilon --genome ${runID}_spades/scaffolds.fasta --bam bwa_mapping_sorted.bam --output $runID --outdir ${runID}_pilon --vcf

## pipeline verified May 30th 2022
## EOF