Explore projects

A modular Snakemake workflow for assembling and quality-checking bacteriophage genomes from Oxford Nanopore long-read sequencing data.

A reproducible Snakemake workflow for end-to-end de novo assembly and quality control of bacteriophage Illumina sequencing datasets. Starting from raw paired-end reads, the pipeline produces assembled genomes, virome classification scores, completeness estimates, terminal-repeat predictions, and a unified HTML + PDF report. A reproducible Snakemake workflow for end-to-end de novo assembly and quality control of bacteriophage Illumina sequencing datasets. Starting from raw paired-end reads, the pipeline produces assembled genomes, virome classification scores, completeness estimates, and a unified HTML + PDF report.

Adaptation of LNPR for carbon modelling:

includes scripts for transfer to carbon input includes uv to initiate R runs in jupyter lab

A Snakemake pipeline for Ralstonia solanacearum species complex (RSSC) sequevar typing based on the endoglucanase (egl) gene. The pipeline extracts the egl gene from bacterial genome assemblies via in-silico PCR, trims it to the ~698 nt phylogenetically informative region, aligns query sequences with curated reference sequevars, builds a maximum-likelihood phylogenetic tree, and produces an annotated tree visualization. Finally, it assigns a sequevar to each query genome based on the nearest reference in the tree. This workflow enables rapid and reproducible sequevar typing for RSSC genomes.

run_epcr.py is a Python script for batch in-silico PCR and probe finding. It scans an input directory for genome FASTA files and runs in-silico PCR on each file in parallel, reporting amplicons and probe matches.

This repository contains files and scripts for analysis of Pseudomonas syringae genomes isolated from citrus plants.

A lightweight, web-based bioinformatics tool for evaluating oligonucleotide sequences used in qPCR assays. Built to support researchers with fast, accurate analysis of primer/probe sets, this tool is compatible with Thermo Fisher qPCR design guidelines, and includes salt-corrected thermodynamic calculations.

A comprehensive Snakemake workflow for assembling high-quality bacterial genomes from Oxford Nanopore long-read sequencing data. The pipeline integrates Autocycler consensus assembly with multiple assemblers (Canu, Flye, Plassembler), performs quality control with Filtlong and Porechop, applies Racon polishing, and provides comprehensive quality assessment using QUAST, BUSCO, and CheckM2. All steps are containerized with conda environments for reproducible results. They include automated HTML/PDF/TXT reporting.

This repository contains a Snakemake bacterial assembly QC pipeline to perform quality control. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries.