Workflows

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)

Workflow for read quality control and trimming.

Steps:

• FastQC (read quality control)

• fastp (read quality trimming)

• bbduk used for rrna filtering

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)

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)

Amplicon analysis workflow using NG-Tax

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