Richard Lupat
SEEK ID: https://workflowhub.eu/people/152
Location:
Australia
ORCID:
https://orcid.org/0000-0002-6435-7100
Joined: 19th Jul 2021
Expertise: Not specified
Tools: Not specified
Roles
Team Administrator
Their tagsRelated items
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.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
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/
This is a genomics pipeline to do a single germline sample variant-calling, adapted from GATK Best Practice Workflow.
This workflow is a reference pipeline for using the Janis Python framework (pipelines assistant).
- Alignment: bwa-mem
- Variant-Calling: GATK HaplotypeCaller
- Outputs the final variants in the VCF format.
Resources
This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:
Type: Janis
Creators: Richard Lupat, Michael Franklin; Jiaan Yu; Juny Kesumadewi
Submitter: Richard Lupat
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