Tracy Chew

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.

Germline-ShortV @ NCI-Gadi is an implementation of the BROAD Institute's best practice workflow for germline short variant discovery. This implementation is optimised for the National Compute Infrastucture's Gadi HPC, utilising scatter-gather parallelism to enable use of multiple nodes with high CPU or memory efficiency. This workflow requires sample BAM files, which can be generated using the Fastq-to-bam @ NCI-Gadi pipeline. Germline-ShortV can be applied ...

Somatic-ShortV @ NCI-Gadi is a variant calling pipeline that calls somatic short variants (SNPs and indels) from tumour and matched normal BAM files following GATK's Best Practice Workflow. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel. ...

Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...

The Flashlite-Supernova pipeline runs Supernova to generate phased whole-genome de novo assemblies from a Chromium prepared library on University of Queensland's HPC, Flashlite.

Infrastructure_deployment_metadata: FlashLite (QRISCloud)

Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...