antismash

BGCViz - a shiny web app, which uses genomic coordinates of BGCs from different sources for a comprehensive comparison.

Parser for antiSMASH output GenBank files.

Reusable bacterial genome mining pipeline for assembled genome FASTA files using QUAST, Bakta, antiSMASH, GECCO, and combined BGC summary reporting.

Custom Bash Shell scripts for use with AntiSMASH and Biosynthetic MetaSpades data outputs (fasta/GenBank). Scripts carry out file management, data parsing and data QC

A pangenomic pipeline interrogating Campylobacter jejuni bacteriocin biosynthetic capacity, revealing a strict absence of classical systems and the presence of orphan Peptidase_C39 leader-cleavage machinery across an epsilon-proteobacterial cohort.

QC-locked genome-mining workflow for prioritising putatively novel biosynthetic gene cluster families using BiG-SCAPE/MiBIG outputs and conservative annotation-derived evidence.

A REST-like API for running antiSMASH style jobs

A web UI for the fungal version of antiSMASH.

My final thesis project work from my Biomedical Genomics MSc undertaken at NUIG, 2021. Includes Nextflow, Snakemake, Bash, Python and R scripts.