Workflows
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Common Workflow Language14
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Genomics4
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14
Workflows visible to you, out of a total of 14
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
Download
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)
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)
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
