Bart Nijsse

An open infrastructure for exploring new horizons for research on microbial communities.

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

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: - workflowquality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - samto_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 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)