Leah Kemp
SEEK ID: https://workflowhub.eu/people/228
Location:
Australia
ORCID: Not specified
Joined: 7th Jan 2022
Expertise: Not specified
Tools: Not specified
Roles
Team Administrator
Space Administrator
Their tagsRelated items
The Institute of Environmental Science and Research (Te Whare Manaaki Tangata, Taiao hoki) is a New Zealand Crown Research Institute (CRI). Its purpose is to deliver scientific and research services to the public health, food safety, security and justice systems, and the environmental sector to improve the safety of, and contribute to the economic, environmental and social well-being of people and communities in New Zealand.
Teams: Genomics - ESR
Web page: https://www.esr.cri.nz/
We develop, adopt and apply new genomics technologies, methods and algorithms to shed new light on the genome and improve the diagnosis of genomic disease.
Space: Garvan Institute of Medical Research
Public web page: https://www.garvan.org.au/research/labs-groups/deveson-lab
Pipeface
Overview
Pipefaceee.
Nextflow pipeline to process long read ONT and/or pacbio HiFi data.
Pipeface's future hold's mitochondrial, STR, CNV and tandem repeat calling.
Workflow
Singleton
%%{init: {'theme':'dark'}}%%
flowchart LR
input_data("Input data: ONT fastq.gz and/or ONT fastq and/or ONT uBAM and/or pacbio HiFi uBAM")
merging{{"Merge runs (if needed)"}}
alignment{{"bam to fastq conversion (if needed), alignment,
...
Type: Nextflow
Creators: Leah Kemp, Andre Reis, Ira Deveson, Kisaru Liyanage, Matthew Downton, Hardip Patel, Kirat Alreja, This is a highly collaborative project, with many contributions from the Genomic Technologies Lab. Notably, Dr Andre Reis and Dr Ira Deveson are closely involved in the development of this pipeline. Optimisations involving DeepVariant and DeepTrio have been contributed by Dr Kisaru Liyanage and Dr Matthew Downton from the National Computational Infrastructure, with support from Australian BioCommons as part of the Workflow Commons project. Haploid-aware mode has been contributed by Dr Hardip Patel & Kirat Alreja from the National Centre for Indigenous Genomics. The installation and hosting of software used in this pipeline has and continues to be supported by the Australian BioCommons Tools and Workflows project (if89).
Submitter: Leah Kemp
