This page includes bioinformatics pipelines, software, and training material developed by the Sydney Informatics Hub, which is a Core Research Facility of the University of Sydney. The Sydney Informatics Hub is an official node of Australian BioCommons.
Many of the resources available here are focused on making processing data at scale more accessible. To achieve this we have developed optimised pipelines for national HPC infrastructures and resources for workflow development.
- ✏️ Bioinformatics training
- 💻 Data processing pipelines
- 📓 Analytical notebooks
- ✨ Supporting Nextflow
- 💾 Software and helper scripts
Bio-toolkit resources- 💁 Cite us to support us
We deliver free training to a national audience. See our training webpage for our events and materials.
Our pipelines have been optimised for compute platforms including the National Compute Infrastructure (NCI) and Pawsey Supercomputing Research Centre's HPC Setonix.
You can find all our pipelines at the Sydney Informatics Hub's WorkflowHub page.
We also support the use of nf-core workflows. Check out the institutional configs we've build for Australian HPC and cloud infrastructures.
| Notebook | Description |
|---|---|
| Rnaseq: differential expression | A Rmarkdown notebook to convert raw gene counts to functional enrichments |
| single cell RNAseq: differential expression etc | A Rmarkdown notebook to convert raw counts to functional enrichments |
| Proteomics: differential abundance | Currently under development |
We have created resources to support Nextflow workflow development and deployment on HPC infrastructures.
| Tool | Description |
|---|---|
| Nextflow DSL2 template | A straightforward Nextflow workflow template generator. |
| Institutional nf-core configs | Public config files for running nf-core pipelines at NCI and Pawsey infrastructures. |
We have created resources to support workflow development and deployment on HPCs, resource benchmarking, and flexible data visualisation.
| Tool | Description |
|---|---|
| HPC usage reports | Pull resource usage data from HPC job logs into reports. |
| NCI Gadi benchmarking template | Automated submission of identical benchmark tasks with increasing compute resources. |
| IGVreport-nf | Generate IGV report for a set of variants. |
| split-GeneWiz-fastq | Split GeneWiz 'combined' (concatenated) fastq files into correct flowcell-lane pairs. |
| Fix-BAM-read-groups | Change the read group metadata within a BAM file. Operates on the header as well as the individual SAM output lines. |
Acknowledgements (and co-authorship, where appropriate) are an important way for us to demonstrate the value we bring to your research. Your research outcomes are vital for ongoing funding of the Sydney Informatics Hub and national compute facilities. Please cite the pipeline repository(s) that you have used. You can also find DOIs for all our pipelines at the Sydney Informatics Hub's WorkflowHub.
Suggested acknowledgements:
Sydney Informatics Hub
The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney and Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia.
NCI
This research was conducted on resources of the National Computational Infrastructure (NCI), an NCRIS-enabled capability supported by the Australian Government. Access to these resources was provided by the Sydney Informatics Hub, a Core Research Facility of The University of Sydney as supported by the Deputy Vice-Chancellor (Research).
Pawsey
This research was conducted on resources of the Pawsey Supercomputing Research Centre, an NCRIS-enabled capability supported by the Australian Government. Access to these resources was provided by the Sydney Informatics Hub, a Core Research Facility of The University of Sydney as supported by the Deputy Vice-Chancellor (Research).