Workflows

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276 Workflows visible to you, out of a total of 287
Stable

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bio.tools Snakemake Deploy Docker image ...

Type: Snakemake

Creators: Ivan Topolsky, Kim Philipp Jablonski

Submitter: Ivan Topolsky

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 ...

Type: Nextflow

Creators: None

Submitter: Alexander Botzki

Work-in-progress

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Nanopore

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

  • Metabat2/MaxBin2/SemiBin
  • DAS Tool
  • CheckM
  • BUSCO
  • GTDB-Tk ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for nanopore read quality control and contamination filtering

  • FastQC before filtering (read quality control)
  • Kraken2 taxonomic read classification
  • Minimap2 read filtering based on given references
  • FastQC after filtering (read quality control)

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 ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Bart Nijsse

Work-in-progress

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 ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Stable

Workflow for Illumina paired read quality control, trimming and filtering

Multiple paired datasets will be merged into single paired dataset.

Summary:

  • FastQC on raw data files
  • fastp for read quality trimming
  • BBduk for phiX and (optional) rRNA filtering
  • Kraken2 for taxonomic classification of reads (optional)
  • BBmap for (contamination) filtering using given references (optional)
  • FastQC on filtered (merged) data

Other UNLOCK workflows on WorkflowHub: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

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

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