Workflows
What is a Workflow?Filters
This workflow is based on the idea of comparing different gene sets through their semantic interpretation. In many cases, the user studies a specific phenotype (e.g. disease) by analyzing lists of genes resulting from different samples or patients. Their pathway analysis could result in different semantic networks, revealing mechanistic and phenotypic divergence between these gene sets. The workflow of BioTranslator Comparative Analysis compares quantitatively the outputs of pathway analysis, ...
BioTranslator performs sequentially pathway analysis and gene prioritization: A specific operator is executed for each task to translate the input gene set into semantic terms and pinpoint the pivotal-role genes on the derived semantic network. The output consists of the set of statistically significant semantic terms and the associated hub genes (the gene signature), prioritized according to their involvement in the underlying semantic topology.
Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures
The Flashlite-Supernova pipeline runs Supernova to generate phased whole-genome de novo assemblies from a Chromium prepared library on University of Queensland's HPC, Flashlite.
Infrastructure_deployment_metadata: FlashLite (QRISCloud)
Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...
Type: Shell Script
Creators: Tracy Chew, Rosemarie Sadsad, Georgina Samaha, Cali Willet
Submitter: Tracy Chew
Flashlite-Juicer is a PBS implementation of Juicer for University of Queensland's Flashlite HPC.
Infrastructure_deployment_metadata: FlashLite (QRISCloud)
Type: Shell Script
Creators: Tracy Chew, Rosemarie Sadsad, Nathaniel Butterworth
Submitter: Tracy Chew
Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. ...
Type: Shell Script
Creators: Georgina Samaha, Rosemarie Sadsad, Tracy Chew, Matthew Downton, Andrey Bliznyuk, Rika Kobayashi, Ben Menadue, Ben Evans
Submitter: Tracy Chew
microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.
To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...
Type: Nextflow
Creators: Valentine Murigneux, Leah W Roberts, Brian M Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D Irwin, Patrick N A Harris, David L Paterson, Mark A Schembri, David M Whiley, Scott A Beatson
Submitter: Valentine Murigneux