A Nextflow-Based Automated Pipeline for Viral Assembly and Characterisation (EVEREST)

EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion) is a comprehensive, end-to-end pipeline designed for virus discovery and characterization. Implemented in Nextflow, it processes Illumina single- and paired-end reads through five key phases: pre-processing, filtering, de novo assembly, refinement, and classification. The pipeline ensures high-quality data by trimming, removing host sequences, eliminating duplicates, and applying digital normalization. It then assembles viral genomes using a de novo assembly strategy, clusters similar contigs, captures viral genomes, and assesses their quality. Finally, EVEREST classifies viral contigs using the NCBI (nucleotide) and Uniprot (amino acid) databases, providing a robust framework for identifying and characterizing viruses from sequencing data.