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ABLeS available software and reference data

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.

In order to load any modules from if89, you need to prepend the directory of if89's modules to the MODULEPATH environment variable using the following command:
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

Please see documentation for more information.


Containers

Will be available soon.


Workflows

Will be available soon.


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

Hardip Patel If89 contributor

Hardip Patel

National Centre for Indigenous Genomics, John Curtin School of Medical Research, The Australian National University

Ziad Al Bkhetan Technical/engagement

Ziad Al Bkhetan

Australian BioCommons, University of Melbourne

J King Chang If89 contributor

J King Chang

School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW, Sydney

Andre Martins Reis If89 contributor

Andre Martins Reis

Garvan Institute of Medical Research

HG

Hasindu Gamaarachchi

Kyle Drover If89 contributor

Kyle Drover

Tim Amos If89 contributor

Tim Amos

Garvan Institute of Medical Research

Kisaru Liyanage If89 contributor

Kisaru Liyanage

National Computational Infrastructure (NCI)

TB
If89 contributor

Terry Bertozzi

South Australian Museum

JS
If89 contributor

Javed Shaikh

National Computational Infrastructure (NCI), Australian National University (ANU)

Kirat Alreja If89 contributor

Kirat Alreja

National Centre for Indigenous Genomics, Australian National University

Leah Kemp If89 contributor

Leah Kemp

Garvan Institute of Medical Research

AB
If89 contributor

Andrey Bliznyuk

National Computational Infrastructure (NCI)

Hyungtaek Jung If89 contributor

Hyungtaek Jung

National Centre for Indigenous Genomics, Australian National University

Wenjing Xue If89 contributor

Wenjing Xue

National Computational Infrastructure (NCI)

Johan Gustafsson Engagement

Johan Gustafsson

Australian BioCommons, University of Melbourne

Dale Roberts If89 contributor

Dale Roberts

National Computational Infrastructure (NCI) (at the time of this work), ARC Centre of Excellence for Climate Extremes