Workflows

What is a Workflow?
13 Workflows visible to you, out of a total of 13
Work-in-progress

Workflow for NonSpliced RNAseq data with multiple aligners.

Steps:

  • workflow_quality.cwl:
  • FastQC (control)
  • fastp (trimming)
  • bowtie2 (read mapping)
  • sam_to_sorted-bam
  • featurecounts (transcript read counts)
  • kallisto (transcript [pseudo]counts)

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Stable

Amplicon analysis workflow using NG-Tax

Steps:

  • Quality control on the reads
  • Execute NGTax for ASV detection and classification

For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse, Jesse van Dam, Peter Schaap,

Submitter: Jasper Koehorst

Work-in-progress

Workflow to build different indices for different tools from a genome and transcriptome.

This workflow expects an (annotated) genome in GBOL ttl format.

Steps:

  • SAPP: rdf2gtf (genome fasta)
  • SAPP: rdf2fasta (transcripts fasta)
  • STAR index (Optional for Eukaryotic origin)
  • bowtie2 index
  • kallisto index

Type: Common Workflow Language

Creator: Bart Nijsse

Submitter: Bart Nijsse

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