Workflows

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

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)

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)

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

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