Pipeline overview

The pipeline is built using Nextflow and processes data in the following steps:

• FastQC : Read quality control.

• fastp : Adapter trimming.

• Kraken2 : Taxonomic classification.

• Bowtie 2 : Read alignment versus the SARS-CoV-2 Wuhan genome.

• SAMtools : Sort and index alignments.

• iVar trim : Primer sequence removal.

• Freyja : Recovering of relative lineage abundances.

• Qualimap : Quality control of alignment.

• iVar variants : Variant calling.

• SnpEff and SnpSift : Variant annotation.

With all the intermediate outputs from the steps above, the pipeline produces several reports aggregating the results in a comprehensible and elegant manner:

• Sample reports: Aggregated report of all the relevant information for each sample (QC, lineages present, etc).

• MultiQC : Interactive aggregated report of all the quality control metrics.

Finally, the pipeline takes all the aforementioned outputs and produces a easily downloadable ZIP file.