The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Web page: https://www.biocommons.org.au/
Funding details:Core funding for the Australian BioCommons comes from the National Collaborative Research Infrastructure Strategy (NCRIS) via Bioplatforms Australia, which is subcontracted to The University of Melbourne as the lead agent. This core funding is amplified through coinvestment from BioCommons partners https://www.biocommons.org.au/funding
Related items
Teams: Australian BioCommons
Organizations: Australian BioCommons

Teams: Australian BioCommons, Sydney Informatics Hub
Organizations: Australian BioCommons, The University of Sydney
Teams: Australian BioCommons, Galaxy Australia
Organizations: University of Melbourne, Australian BioCommons

Expertise: Biochemistry, Proteomics, Mass Spectrometry Imaging
Tools: Mass spectrometry, Proteomics
Teams: Australian BioCommons
Organizations: University of Melbourne, Australian BioCommons

Teams: QCIF Bioinformatics, Galaxy Australia
Organizations: QCIF

Teams: Australian BioCommons
Organizations: Australian BioCommons
Teams: Galaxy Australia, QCIF Bioinformatics
Organizations: QCIF

Teams: Sydney Informatics Hub
Organizations: The University of Sydney

Teams: QCIF Bioinformatics
Organizations: QCIF
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
Organisms: Not specified
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.
Space: Australian BioCommons
Public web page: https://www.qcif.edu.au/
Organisms: Not specified
Space: Australian BioCommons
Public web page: https://pawsey.org.au/
Organisms: Not specified
Space: Australian BioCommons
Public web page: Not specified
Organisms: Not specified
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy ...
Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
Organisms: Not specified
Janis is an open-source Python framework that aims to address the portability and interoperability problems between workflow specifications, by abstracting both the workflow and execution model in order to generate CWL, WDL or Nextflow workflows.
Funding sources:
- Institutional financial support for software engineering and academic contributions from Peter Mac and Melbourne Bioinformatics
- Richard Lupat was supported by a grant from the Peter Mac Foundation
- Bernard Pope was supported by a ...
Space: Australian BioCommons
Public web page: https://janis.readthedocs.io/
Organisms: Not specified
We are a team of Academic Specialists who collaborate with researchers to enable data-intensive research across the University. We work with researchers at all stages of the research lifecycle, from research design and data collection, all the way through to analysis, visualisation, and interpretation.
Space: Australian BioCommons
Public web page: https://mdap.unimelb.edu.au/
Organisms: Not specified
Abstract (Expand)
Authors: V. Murigneux, L. W. Roberts, B. M. Forde, M. D. Phan, N. T. K. Nhu, A. D. Irwin, P. N. A. Harris, D. L. Paterson, M. A. Schembri, D. M. Whiley, S. A. Beatson
Date Published: 25th Jun 2021
Publication Type: Journal
PubMed ID: 34172000
Citation: BMC Genomics. 2021 Jun 25;22(1):474. doi: 10.1186/s12864-021-07767-z.
This document is adapted from the 16S tutorials available at Galaxy [https://training.galaxyproject.org/training-material/topics/metagenomics/ tutorials/mothur-miseq-sop-short/tutorial.html] and [https://training.galaxyproject.org/training-material/ topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html]. Please also go through these tutorials for better understandings. Note: The steps mentioned in this document are well suited for V3-V4 regions. However the parameters could be varied if ...
Creators: Ahmed Mehdi, Saskia Hiltemann, Bérénice Batut, Dave Clements
Submitter: Sarah Williams
The aim of this workflow is to handle the routine part of shotgun metagenomics data processing on Galaxy Australia.
The workflow is using the tools MetaPhlAn2 for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes. The workflow is based on the Galaxy Training tutorial 'Analyses of metagenomics data - The global picture' (Saskia Hiltemann, Bérénice Batut) https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data. ...
Type: Galaxy
Creators: Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut, The workflow is based on the Galaxy Training tutorial Analyses of metagenomics data. Thank you to the Galaxy Australia team, Igor Makunin and Mike Thang for help with the workflow
Submitter: Valentine Murigneux
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
16S Microbial Analysis with mothur (short)
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Type: Galaxy
Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi
Submitter: Sarah Williams
Loads a single cell counts matrix into an annData format - adding a column called sample with the sample name. (Input format - matrix.mtx, features.tsv and barcodes.tsv)
Basic processing of a QC-filtered Anndata Object. UMAP, clustering e.t.c
Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.
Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.
From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData
Take a scRNAseq counts matrix from a single sample, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData object.
From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData
Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.
HiFi de novo genome assembly workflow
HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.
Please refer to the following documentation for detailed description of each workflow section:
- [Adapter filtration and pre-assembly quality control ...
Type: Nextflow
Creators: Naga Kasinadhuni, Ziad Al Bkhetan, Martha Zakrzewski, Kenneth Chan, Uwe Winter, Johan Gustafsson
Submitter: Johan Gustafsson
Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics
IGVreport-nf
- Description
- Diagram
- User guide
- Workflow summaries
- Metadata
- Component tools
- Required (minimum) inputs/parameters
- Additional notes
- Help/FAQ/Troubleshooting
- Acknowledgements/citations/credits
Description
Quickly generate [IGV .html
...
GermlineStructuralV-nf
:wrench: This pipeline is currently under development :wrench:
- Description
- Diagram
- User guide
- Infrastructure usage and recommendations
- Benchmarking
- Workflow summaries
- Metadata
- Component tools
- Additional notes
- Help/FAQ/Troubleshooting
...
Type: Nextflow
Creators: Georgina Samaha, Marina Kennerson, Tracy Chew, Sarah Beecroft
Submitter: Georgina Samaha
PacBio HiFi genome assembly using hifiasm v2.1
General usage recommendations
Please see the Genome assembly with hifiasm on Galaxy Australia guide.
See change log
Acknowledgements
The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...