Workflows

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280 Workflows visible to you, out of a total of 291

This workflow is designed to analyze to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies. (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant ...

Type: Nextflow

Creators: Anna Niehues, Casper de Visser

Submitter: Casper de Visser

COVID-19: consensus construction

This workflow aims at generating reliable consensus sequences from variant calls according to transparent criteria that capture at least some of the complexity of variant calling.

It takes a collection of VCFs (with DP and DP4 INFO fields) and a collection of the corresponding aligned reads (for the purpose of calculating genome-wide coverage) such as produced by any of the variant calling workflows in ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

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 ...

Type: Galaxy

Creators: Gareth Price, Katherine Farquharson

Submitter: Johan Gustafsson

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

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

COVID-19: variation analysis reporting

This workflow takes VCF datasets of variants produced by any of the "*-variant-calling" workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular reports of variants by samples and by variant, along with an overview plot of variants and their allele-frequencies across all samples.

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

ChIP-seq paired-end Workflow

Inputs dataset

  • The workflow needs a single input which is a list of dataset pairs of fastqsanger.

Inputs values

  • adapters sequences: this depends on the library preparation. If you don't know, use FastQC to determine if it is Truseq or Nextera.
  • reference_genome: this field will be adapted to the genomes available for bowtie2.
  • effective_genome_size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).

...

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

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