jlumpe/tomdeman-genomics_workflow

Bacterial assembly and annotation pipeline

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/*

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Trimming PhiX free reads using Trimmomatic

Usage

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

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Assembling contigs from PhiX free and trimmed reads using SPAdes

Usage

perl run_SPAdes.pl directory/containing/trimmed/and/virus/free/reads/only/*

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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/*

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Perform all four steps indicated above (bbduk-Trimmomatic-SPAdes-PlasmidSPAdes) plus BUSCO genome assembly QC, and Prokka gene annotation using one Bash script. Prokka will only annotate contigs of 500bp and larger (contigs are filtered using contig_size_select.pl)

Usage

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

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