Workflows

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6 Workflows visible to you, out of a total of 6
Work-in-progress

Workflow for Metagenomics from raw reads to annotated bins.

Steps:

  • workflow_quality.cwl:

  • FastQC (control)

  • fastp (trimming)

  • Kraken2 (Taxonomic Read Classification

  • SPAdes (Assembly)

  • QUAST (Assembly quality report)

  • BBmap (Read mapping to assembly)

  • samtobam (sam to indexed bam)

  • metabatContigDepths (jgisummarizebamcontigdepths)

  • MetaBat2 (binning)

Type: Common Workflow Language

Creators: None

Submitter: Jasper Koehorst

Work-in-progress

Workflow for read quality control and trimming.

Steps:

  • FastQC (read quality control)

  • fastp (read quality trimming)

  • bbduk used for rrna filtering

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for NonSpliced RNAseq data with multiple aligners.

Steps:

  • workflow_quality.cwl:

  • FastQC (control)

  • fastp (trimming)

  • bowtie2 (read mapping)

  • samtosorted-bam

  • featurecounts (transcript read counts)

  • kallisto (transcript [pseudo]counts)

Type: Common Workflow Language

Creator: Bart Nijsse

Submitter: Bart Nijsse

Work-in-progress

Workflow for Spliced RNAseq data

Steps:

  • workflow_quality.cwl:

  • FastQC (Read Quality Control)

  • fastp (Read Trimming)

  • STAR (Read mapping)

  • featurecounts (transcript read counts)

  • kallisto (transcript [pseudo]counts)

Type: Common Workflow Language

Creator: Bart Nijsse

Submitter: Bart Nijsse

Stable

Amplicon analysis workflow using NG-Tax

Type: Common Workflow Language

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

Creators: None

Submitter: Bart Nijsse

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