Australian BioCommons Tools and Workflows project (if89)

This page provides a comprehensive overview of tools, containers, workflows, and datasets available to ABLeS researchers through the Australian BioCommons Tools and Workflows project (project if89 @ NCI).

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.

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 Aug 2025) 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.
Kraken2	Kraken 2, KrakenUniq and Bracken indexes	9 Jun 2025	`kraken2/09062025/k2_core_nt`	Kraken2 Very large collection, inclusive of GenBank, RefSeq, TPA and PDB.
Kraken2	Kraken 2, KrakenUniq and Bracken indexes	9 Jun 2025	`kraken2/09062025/k2_standard`	Kraken2 pre-built "standard" database, includes RefSeq archaea, bacteria, viral, plasmid, human, plus UniVec_Core.
Dfam	Dfam	04 Aug 2025	`dfam/04082025/dfam39`	Dfam 3.9; FamDB Format 2.0; Partition 7 [dfam39_full.7.h5]: Mammalia (57 GB) More info - https://www.dfam.org/releases/Dfam_3.9/families/FamDB/README.txt. Available with RepeatMasker/4.2.0 (if89 module)
Human reference genome	GRCh38.p14	Feb 2022	`Homo_Ref/GRCh38.p14`	Homo sapiens reference genome GRCh38 patch release 14 (GCF_000001405.40). Includes primary assembly FASTA, gene annotation (GTF), transcript and protein FASTA files from NCBI RefSeq. This assembly is the current standard reference for WGS/WES alignment, variant calling, and annotation pipelines (e.g. BWA-MEM2, GATK, DeepVariant, VEP).
Human reference genome	GRCh37.p13	Feb 2014	`Homo_Ref/GRCh37.p13`	Homo sapiens reference genome GRCh37 patch release 13 (GCF_000001405.25), maintained for backward compatibility with legacy datasets and resources (e.g. older GWAS, ExAC, early gnomAD releases). Includes primary assembly FASTA, gene annotation (GTF), transcript and protein FASTA files from NCBI RefSeq.