How to cite this guide
If you use this guide in your research or training, please cite it as:
O’Brien M, Jaya F, Xue W, Al Bkhetan Z, Botting A, Gustafsson J. Samaha G (2026). BioShell how-to guide. Australian BioCommons. [AUTHOR TO SUPPLY — Zenodo DOI once minted]
[AUTHOR TO SUPPLY — add bio.tools entry URL once registered]
[AUTHOR TO SUPPLY — add WorkflowHub entry URL once registered]
Contributors
| Name | GitHub | ORCID |
|---|---|---|
| Mitchell O’Brien | @Mitchob | 0000-0003-0662-9101 |
| Fred Jaya | @fredjaya | 0000-0002-4019-7026 |
| Georgina Samaha | @georgiesamaha | 0000-0003-0419-1476 |
| Wenjing Xue | @eileen-xue | — |
| Ziad Al Bkhetan | @ziadbkh | 0000-0002-4032-5331 |
| Andy Botting | @andybotting | — |
| Johan Gustafsson | @supernord | 0000-0002-2977-5032 |
Acknowledgements
The authors acknowledge the support of Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia funding.
This guide makes use of the ELIXIR toolkit theme.
This guide is part of the ABLeS programme, which supports life science research computing across Australian national infrastructure. BioShell is available through ARDC Nectar Research Cloud and NCI Nirin.
References
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Gustafsson J, et al. (2023). Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons Leadership Share (3.0). Zenodo. https://doi.org/10.5281/zenodo.10139651
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CernVM-FS documentation. https://cvmfs.readthedocs.io/en/stable/
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Singularity Registry HPC (SHPC) documentation. https://singularity-hpc.readthedocs.io/
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BioContainers registry. https://biocontainers.pro/registry
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Galaxy Project CVMFS repositories. https://galaxyproject.org/admin/cvmfs/
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Nextflow documentation. https://www.nextflow.io/docs/latest/
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nf-core community. https://nf-co.re/
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FastQC. https://bio.tools/fastqc
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samtools. https://bio.tools/samtools
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plink. https://bio.tools/plink
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bwa. https://bio.tools/bwa
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STAR. https://bio.tools/star
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SPAdes. https://bio.tools/spades
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GATK. https://bio.tools/gatk