Fig. 1

Pipeline overview. Central panel: DNAscan accepts sequencing data, and optionally variant files. The pipeline firstly performs an alignment step (details in the left panel), followed by a customisable data analysis protocol (details in the right panel). Finally, results are annotated and user-friendly QC and result reports are generated. The annotation step uses Annovar to enrich the results with functional information from external databases. Right panel: detailed description of the post alignment analysis pipeline. Aligned reads are used by the variant calling pipeline (Freebayes + GATK HC); both aligned and unaligned reads are used by Manta and ExpensionHunter (for which repeat description files have to be provided) to look for structural variants. The unaligned reads are mapped to a database of known viral genomes (NCBI database) to screen for their DNA in the input sequencing data. Left panel: Alignment stage description. Raw reads are aligned with HISAT2. Resulting soft-clipped and unaligned reads are realigned with BWA mem and then merged with the others using Samtools