A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.

A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.

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).