Additional file 1. Supplemental Text: Analysis of viral GenBank records demonstrated the advent of NGS in viral sequencing in the last two decades. Supplement Figure S1. Workflow diagrams of simulated data from data creation through de novo assembly. Supplement Figure S2. Analysis of the final contig assembly graphs for a clinical sample containing enterovirus A71 (EV-A71) variants using Bandage. Supplement Figure S3. Assembly with three simulated variants. Supplement Table S1. Total counts from NCBI’s GenBank non-redundant nucleotide database. Supplement Table S2. Total count of sequencing technologies for sequences >2000 nt in the NCBI GenBank non-redundant nucleotide database for years 2012–2019. Supplement Table S3. Total counts from NCBI’s GenBank non-redundant nucleotide database with multiple sequencing technologies listed per entry. Supplement Table S4. Total counts from NCBI’s GenBank non-redundant nucleotide database of all entries with three and four sequencing technologies listed. Supplement Table S5. Total count of assembly programs used to generate sequences >2000 nt in the NCBI GenBank non-redundant nucleotide database. Supplement Table S6. The 10 de novo assemblers used for analysis of the simulated data, as categorized by their underlying assembly algorithms.