Fig. 1

Flowchart describing processes and steps performed by HAVoC pipeline. The pipeline constructs consensus sequences from all FASTQ files in an input directory and then compares the resulting sequences to other established SARS-CoV-2 genomes to assign them the most likely lineages. The pipeline requires a FASTA file of adapter sequences for FASTQ pre-processing and a reference genome of SARS-CoV-2 in a separate FASTA file. The adapter file is not required when running the pipeline with fastp option. Input files are highlighted in green and the outputs in red