Kisaru Liyanage
SEEK ID: https://workflowhub.eu/people/906
Location:
Australia
ORCID: Not specified
Joined: 4th Dec 2024
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, National Computational Infrastructure (NCI) WorkflowHub team
Web page: https://www.biocommons.org.au/
The National Computational Infrastructure (NCI) is one of Australia’s leading Tier-1 facilities for high-performance computing, data, and storage. It provides specialised services to support bioinformatics workflows, alongside a wide range of applications in science, government, and industry.
Space: Australian BioCommons
Public web page: https://nci.org.au
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
Nextflow Pipeline for DeepVariant
This repository contains a Nextflow pipeline for Google’s DeepVariant, optimised for execution on NCI Gadi.
Quickstart Guide
- Edit the
pipeline_params.ymlfile to include:
samples: a list of samples, where each sample includes the sample name, BAM file path (ensure corresponding .bai is in the same directory), path to an optional regions-of-interest BED file (set to''if not required), and the model type.ref: path to the reference FASTA (ensure ...
