This page provides a comprehensive overview of tools, containers, workflows, and datasets available to ABLeS researchers. It also includes information about the Australian BioCommons Tools and Workflows project (if89), which serves as a shared repository for bioinformatics tools and workflows.
Pawsey Supercomputing Centre
Software
There is a wide range of centrally installed software for Setonix users, including popular bioinformatics tools. More information about software on Setonix.
Setonix users can also install their choice of software on the /software partition. We also encourage usage of containers with Singularity. Users are able to download any containers they like!
Reference datasets
Popular bioinformatics reference datasets are available on Pawsey. Additional reference sets can be requested via help@pawsey.org.au
National Computational Infrastructure (NCI)
Centrally supported software (/apps)
Centrally supported software available through NCI can be viewed here.
Shared repository of tools and software (project if89 on NCI)
Users at NCI also have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This is a repository of popular tools, containers and workflows that can be used by anyone in the NCI system.
Anyone from an NCI project is also invited to contribute to if89, and add more software installations that can be shared with others.
Software
The list of tools available through the Australian BioCommons Shared Tools and Workflows repository (NCI (if89)) is available through ToolFinder.
module use -a /g/data/if89/apps/modulefiles After that, you can load any tool, then utilising it directly using the following command:
module load $tool/$version You can list all available modules using the following command:
module available
Containers
Workflows
Software databases
Some of the databases required by different bioinformatics software tools are made available through the if89 project.
They are located at /g/data/if89/data_library. You can request other databases to be included by contacting us.
A list of the currently available (as of 25 Jan 2023) databases is included below:
| Dataset | Source | Download date | Location | Details |
|---|---|---|---|---|
| Blast | Blast Webpage | 28 Aug 2022 | blast_db/28082022/ |
nr.*.gz: non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB, and RefSeq. nt.*.gz: nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ. |
| Blast | Blast Webpage | 7 Nov 2023 | blast_db/07112023 |
nt.*: nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ. |
| Alphafold/UniProt | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/UniProt/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
| Alphafold/UniProt-NO-CA | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/UniProt-NO-CA/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
| Alphafold/UniProt50 | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/UniProt50/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
| Alphafold/Proteome | foldseek github pages and AlphaFold Protein Structure Database webpage | 29 Nov 2022 | AlphaFoldDB/aminoacid/Proteome/29112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
| Alphafold/Swiss-Prot | foldseek github pages and AlphaFold Protein Structure Database webpage | 30 Nov 2022 | AlphaFoldDB/aminoacid/Swiss-Prot/30112022/ |
Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool. |
| Busco/eukaryota_odb10 | Busco webpages | 14 Aug 2023 | busco_db/14082023/lineages |
Lineage datasets for busco tool. Downloaded manually. |
| Kaiju | Kaiju Webpage | 26 May 2023 | kaiju/26052023/kaiju_db_rvdb |
Kaiju pre-built indexes for protein sequences from RVDB-prot v26.0. Contains the Kaiju .fmi index file, as well as nodes.dmp and names.dmp from the NCBI taxonomy. |
| Kraken2 | Kraken 2, KrakenUniq and Bracken indexes | 9 Oct 2023 | kraken2/09102023/k2_pluspf |
Kraken2 pre-built index for RefSeq database (archaea, bacteria, viral, plasmid, human, protozoa & fungi) plus UniVec_Core. |
if89 Contributors
If89 contributor
Hardip Patel
National Centre for Indigenous Genomics, John Curtin School of Medical Research, The Australian National University
Technical/engagement
Ziad Al Bkhetan
Australian BioCommons, University of Melbourne
If89 contributor
J King Chang
School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW, Sydney
If89 contributor
Andre Martins Reis
Garvan Institute of Medical Research
Hasindu Gamaarachchi
If89 contributor
Kyle Drover
If89 contributor
Tim Amos
Garvan Institute of Medical Research
If89 contributor
Kisaru Liyanage
National Computational Infrastructure (NCI)
Terry Bertozzi
South Australian Museum
Javed Shaikh
National Computational Infrastructure (NCI), Australian National University (ANU)
If89 contributor
Kirat Alreja
National Centre for Indigenous Genomics, Australian National University
If89 contributor
Leah Kemp
Garvan Institute of Medical Research
Andrey Bliznyuk
National Computational Infrastructure (NCI)
If89 contributor
Hyungtaek Jung
National Centre for Indigenous Genomics, Australian National University
If89 contributor
Wenjing Xue
National Computational Infrastructure (NCI)
Engagement
Johan Gustafsson
Australian BioCommons, University of Melbourne
If89 contributor
Dale Roberts
National Computational Infrastructure (NCI) (at the time of this work), ARC Centre of Excellence for Climate Extremes