Workflows
What is a Workflow?Filters
Reads2Map
Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases ...
Reads2Map
Reads2Map presents a collection of WDL workflows to build linkage maps from sequencing reads. Each workflow release is described in the [Read2Map releases ...
This Galaxy-E workflow was made from the "Cleaning GBIF data for the use in biogeography" tutorial and allows to:
- Use CoordinateCleaner to automatically flag problematic records
- Use GBIF provided meta-data to improve coordinate quality, tailored to your downstream analyses
- Use automated cleaning algorithms of CoordinateCleaner to identify problematic contributing datasets
- Visualize data ...
Introduction
vibbits/rnaseq-editing is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation followed by a prediction step of editing sites using RDDpred.
The pipeline is largely based on the nf-core RNAseq pipeline.
The initial nf-core pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable ...
Workflow for Metagenomics from bins to metabolic models (GEMs)
Summary
- Prodigal gene prediction
- CarveMe genome scale metabolic model reconstruction
- MEMOTE for metabolic model testing
- SMETANA Species METabolic interaction ANAlysis
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: https://gitlab.com/m-unlock/cwl/workflows
**How ...
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 ...
Workflow Kallisto RNAseq
(pseudoalignment on transcripts)
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- kallisto
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
- 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