Genomics_workflow

An easy bacterial assembly and annotation pipeline

Remove PhiX from raw reads using bbduk

Usage

perl run_bbduk.pl directory/containing/raw/reads/only/*

Trimming PhiX free reads using Trimmomatic

Usage

perl run_trimmomatic.pl directory/containing/PhiX/free/reads/only/*

Assembling contigs from PhiX free and trimmed reads using SPAdes

Usage

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

Usage

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)

Usage

bash bbduk-trimmomatic-SPAdes-plasmidSPAdes-prokka-BUSCO.bash