Working closely with researchers, the QCIF Bioinformatics team apply data management, processing, integration, analysis and visualisation techniques to maximise the potential value of biological and clinical data sets. QCIF Bioinformatics is a partner in the Australian BioCommons.

qcif/taxodactyl is a modular, reproducible Nextflow workflow for the conservative taxonomy assignment to DNA sequences, designed for high-confidence, auditable results in biosecurity and biodiversity contexts. The workflow integrates multiple bioinformatics tools and databases, automates best-practice analysis steps, and produces detailed reports with supporting evidence for each taxonomic assignment.

Workflow Overview

The pipeline orchestrates a series of analytical steps, each encapsulated ...

ONTViSc (ONT-based Viral Screening for Biosecurity)

Introduction

eresearchqut/ontvisc is a Nextflow-based bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity. It takes fastq files generated from either amplicon or whole-genome sequencing using Oxford Nanopore Technologies as input.

The pipeline can either: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly ...