Workflows
What is a Workflow?- deprecated -
Workflow for sequencing with ONT Nanopore, from basecalling to assembly.
- Guppy (basecalling of raw reads)
- MinIONQC (quality check)
- FASTQ merging from multi into one file
- Kraken2 (taxonomic classification)
- Krona (classification visualization)
- Flye (de novo assembly)
- Medaka (assembly polishing)
- QUAST (assembly quality reports)
All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data
Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...
Type: Snakemake
Creators: Ozan Ozisik, Juma Bayjan, Cenna Doornbos, Friederike Ehrhart, Matthias Haimel, Laura Rodriguez-Navas, José Mª Fernández, Eleni Mina, Daniël Wijnbergen
Submitter: Juma Bayjan
For integrative analysis of CAKUT multi-omics data DIABLO method of the mixOmics package (version 6.10.9. Singh et. al. 2019) was used with sPLS-DA (sparse Partial Least Squares Discriminant Analysis Discriminant Analysis) and PLS-DA classification.
Type: Snakemake
Creators: Juma Bayjan, Ozan Ozisik, Cenna Doornbos, Friederike Ehrhart
Submitter: Juma Bayjan
In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.
The peptidome and ...
Type: Snakemake
Creators: Woosub Shin, Friederike Ehrhart, Juma Bayjan, Cenna Doornbos, Ozan Ozisik
Submitter: Juma Bayjan
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 ...
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 ...
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) ...
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.