Workflows

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29 Workflows visible to you, out of a total of 29
Stable

Optional workflow to purge duplicates from the contig assembly.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

Work-in-progress

This is a genomics pipeline to do a single germline sample variant-calling, adapted from GATK Best Practice Workflow.

This workflow is a reference pipeline for using the Janis Python framework (pipelines assistant).

  • Alignment: bwa-mem
  • Variant-Calling: GATK HaplotypeCaller
  • Outputs the final variants in the VCF format.

Resources

This pipeline has been tested using the HG38 reference set, available on Google Cloud Storage through:

Type: Janis

Creators: Richard Lupat, Michael Franklin; Jiaan Yu; Juny Kesumadewi

Submitter: Richard Lupat

Combined workflow for large genome assembly

The tutorial document for this workflow is here: https://doi.org/10.5281/zenodo.5655813

What it does: A workflow for genome assembly, containing subworkflows:

  • Data QC
  • Kmer counting
  • Trim and filter reads
  • Assembly with Flye
  • Assembly polishing
  • Assess genome quality

Inputs:

  • long reads and short reads in fastq format
  • reference genome for Quast

Outputs:

  • Data information - QC, kmers
  • Filtered, trimmed reads
  • Genome assembly, assembly graph, ...

Type: Galaxy

Creator: Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.230.1

Stable
No description specified

Type: Galaxy

Creators: None

Submitter: Mike Thang

Stable

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

Type: Galaxy

Creators: None

Submitter: Mike Thang

Stable

Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

Stable

Conversion of files from BAM to FASTQ, including FASTQC & CCS.BAM file quality control (QC) steps.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

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