Workflows

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280 Workflows visible to you, out of a total of 291
Work-in-progress

Workflow for Metagenomics binning from assembly

Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file

Summary

  • MetaBAT2 (binning)
  • MaxBin2 (binning)
  • SemiBin (binning)
  • DAS Tool (bin merging)
  • EukRep (eukaryotic classification)
  • CheckM (bin completeness and contamination)
  • BUSCO (bin completeness)
  • GTDB-Tk (bin taxonomic classification)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

**All tool CWL ...

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

Submitter: Jasper Koehorst

Workflow Kallisto RNAseq

(pseudoalignment on transcripts)

All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

- Deprecated -

See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367

And other workflows: https://workflowhub.eu/projects/16#workflows

Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning

  • Workflow Nanopore Quality
  • Kraken2 taxonomic classification of FASTQ reads
  • Flye (de-novo assembly)
  • Medaka (assembly polishing)
  • metaQUAST (assembly quality reports)

When Illumina reads are provided:

  • Workflow ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Jasper Koehorst

- 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

Stable

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

Stable

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

Stable

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 ...

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