Workflows
What is a Workflow?Filters
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
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 ...
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.
Type: Nextflow
Creators: Nandan Deshpande, Tracy Chew, Cali Willet, Georgina Samaha
Submitter: Georgina Samaha
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, ...
Type: Nextflow
Creators: Georgina Samaha, Marina Kennerson, Tracy Chew, Sarah Beecroft
Submitter: Georgina Samaha
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
IGVreport-nf
- Description
- Diagram
- User guide
- Workflow summaries
- Metadata
- Component tools
- Required (minimum) inputs/parameters
- Additional notes
- Help/FAQ/Troubleshooting
- Acknowledgements/citations/credits
Description
Quickly generate [IGV .html
...
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 ...
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 ...
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) ...
IndexReferenceFasta-nf
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