Workflows

What is a Workflow?
45 Workflows visible to you, out of a total of 45
Work-in-progress

ONTViSc (ONT-based Viral Screening for Biosecurity)

Introduction

eresearchqut/ontvisc is a Nextflow-based bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity. It takes fastq files generated from either amplicon or whole-genome sequencing using Oxford Nanopore Technologies as input.

The pipeline can either: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly ...

Type: Nextflow

Creators: Marie-Emilie Gauthier, Craig Windell, Magdalena Antczak, Roberto Barrero

Submitter: Magdalena Antczak

DOI: 10.48546/workflowhub.workflow.683.1

Stable

 

Welcome to the pipesnake. Let's get started.


Introduction

pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity ...

Type: Nextflow

Creators: Ziad Al-Bkhetan, Ian Brennan

Submitter: Ziad Al-Bkhetan

Work-in-progress

This is a Nextflow implementaion of the GATK Somatic Short Variant Calling workflow. This workflow can be used to discover somatic short variants (SNVs and indels) from tumour and matched normal BAM files following GATK's Best Practices Workflow. The workflowis currently optimised to run efficiently and at scale on the National Compute Infrastructure, Gadi.

GermlineStructuralV-nf is a pipeline for identifying structural variant events in human Illumina short read whole genome sequence data. GermlineStructuralV-nf identifies structural variant and copy number events from BAM files using Manta, Smoove, and TIDDIT. Variants are then merged using SURVIVOR, ...

Stable

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

  • [Adapter filtration and pre-assembly quality control ...

Type: Nextflow

Creators: Naga Kasinadhuni, Ziad Al-Bkhetan, Martha Zakrzewski, Kenneth Chan, Uwe Winter, Johan Gustafsson

Submitter: Johan Gustafsson

Stable

PacBio HiFi genome assembly using hifiasm v2.1

General usage recommendations

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

See change log

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...

Stable

Purge-duplicates-from-hifiasm-assembly

General recommendations for using Purge-duplicates-from-hifiasm-assembly

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...

Type: Galaxy

Creators: Gareth Price, Gareth Price

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.237.2

Stable

BAM-to-FASTQ-QC

General recommendations for using BAM-to-FASTQ-QC

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) ...

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.220.2

Powered by
(v.1.16.0-main)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH