Workflows

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29 Workflows visible to you, out of a total of 29
Work-in-progress

RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.152.1

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

Stable

microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.

To build microPIPE we evaluated the performance of several tools at each step of bacterial genome assembly, including basecalling, assembly, and polishing. Results at each step were validated using the high-quality ST131 Escherichia coli strain EC958 (GenBank: HG941718.1). After appraisal of each step, we selected the best combination of ...

Type: Nextflow

Creators: Valentine Murigneux, Leah W Roberts,  Brian M Forde, Minh-Duy Phan, Nguyen Thi Khanh Nhu, Adam D Irwin, Patrick N A Harris, David L Paterson, Mark A Schembri, David M Whiley, Scott A Beatson 

Submitter: Valentine Murigneux

DOI: 10.48546/workflowhub.workflow.140.1

Work-in-progress

SLURM HPC Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

  • Using hg38 human reference genome build
  • Running using HPC/SLURM scheduling. This repo was specifically tested on Pawsey Zeus machine, primarily running in the /scratch partition.
  • Starting from short-read Illumina paired-end fastq files as input

Dependencies

The following versions have been ...

Type: Unrecognized workflow type

Creators: None

Submitter: Sarah Beecroft

Work-in-progress

Local Cromwell implementation of GATK4 germline variant calling pipeline

See the GATK website for more information on this toolset

Assumptions

  • Using hg38 human reference genome build
  • Running 'locally' i.e. not using HPC/SLURM scheduling, or containers. This repo was specifically tested on Pawsey Nimbus 16 CPU, 64GB RAM virtual machine, primarily running in the /data volume storage partition.
  • Starting from short-read Illumina paired-end fastq ...

Type: Unrecognized workflow type

Creators: None

Submitter: Sarah Beecroft

Stable

This is a Galaxy workflow that uses to convert the16S BIOM file to table and figures. It is part of the metaDEGalaxy workflow MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.

Type: Galaxy

Creator: Mike Thang

Submitter: Mike Thang

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