Workflows

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7 Workflows visible to you, out of a total of 7

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Jasper Koehorst

DOI: 10.48546/workflowhub.workflow.154.2

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

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for NonSpliced RNAseq data with multiple aligners.

Steps: - workflowquality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - samto_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 for (paired) read quality control, trimming and contamination filtering based on a given reference.

Will output a merged set of read pairs, when multiple datasets are used.

Steps:

  • FastQC (read quality control)

  • fastp (read quality trimming)

  • bbduk used (rrna filtering)

  • bbmap (contamination filter)

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Work-in-progress

Workflow for Metagenomics from raw reads to bins.

Steps:

  • workflow_quality.cwl:

  • FastQC (control)

  • fastp (quality trimming)

  • bbmap contamination filter

  • SPAdes (Assembly)

  • QUAST (Assembly quality report)

  • BBmap (Read mapping to assembly)

  • MetaBat2 (binning)

  • CheckM (bin completeness and contamination)

  • GTDB-Tk (bin taxonomic classification)

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

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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