Workflows

What is a Workflow?
15 Workflows visible to you, out of a total of 15
Work-in-progress

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)

Type: Shell Script

Creators: None

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.151.1

Stable

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 ...

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Georgina Samaha, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.149.1

Stable

Flashlite-Juicer is a PBS implementation of Juicer for University of Queensland's Flashlite HPC.

Infrastructure_deployment_metadata: FlashLite (QRISCloud)

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Nathaniel Butterworth

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.150.1

Work-in-progress

Bootstrapping-for-BQSR @ NCI-Gadi is a pipeline for bootstrapping a variant resource to enable GATK base quality score recalibration (BQSR) for non-model organisms that lack a publicly available variant resource. This implementation is optimised for the National Compute Infrastucture's Gadi HPC. Multiple rounds of bootstrapping can be performed. Users can use Fastq-to-bam @ NCI-Gadi and Germline-ShortV @ NCI-Gadi to ...

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.153.1

Work-in-progress

Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. 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. ...

Type: Shell Script

Creators: Georgina Samaha, Rosemarie Sadsad, Tracy Chew, Matthew Downton, Andrey Bliznyuk, Rika Kobayashi, Ben Menadue, Ben Evans

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.145.1

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