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 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

Alignment, assembly and annotation of generated transcripts from RNASEQ reads.

Alignment, assembly and annotation of RNASEQ reads as well as annotation of generated transcripts.

Alignment, assembly RNASEQ reads and annotation of generated transcripts.

Alignment, assembly and annotation of RNQSEQ reads using TOPHAT (without filtering out host reads).