Remove PhiX from raw reads using bbduk
perl run_bbduk.pl directory/containing/raw/reads/only/*
Trimming PhiX free reads using Trimmomatic
perl run_trimmomatic.pl directory/containing/PhiX/free/reads/only/*
Assembling contigs from PhiX free and trimmed reads using SPAdes
perl run_SPAdes.pl directory/containing/trimmed/and/virus/free/reads/only/*
Assembling plasmid contigs, rather than plasmid chromosomal sequences, from PhiX free and trimmed reads using PlasmidSPAdes
perl run_plasmidSPAdes.pl directory/containing/PhiX_and_contaminant/free/reads/only/*
Perform all four steps indicated above (bbduk-Trimmomatic-SPAdes-PlasmidSPAdes) plus BUSCO genome assembly QC, MLST genotyping, plasmid replicon gene identification, AMR gene detection, and Prokka protein coding gene annotation using one Bash script. Script will only annotate/genotype contigs of 500bp and larger (contigs are filtered using contig_size_select.pl)
bash bbduk-trimmomatic-SPAdes-plasmidSPAdes-prokka-BUSCO.bash