HIV64148 Supplementary data

Figure S1. The MetaQUAST assessment evaluated contigs from the assemblers processing four median read-length FASTQ inputs: (A) 1,000-nt, (B) 2,000-nt, (C) 3,000-nt, and (D) 4,000-nt (Table 3). The x-axis displays the percentage sequence similarity obtained from a BLAST alignment with the corresponding reference genomes, while the y-axis represents the aligned length, indicating the longest continuous alignment between each contig and its reference genome. Dot sizes indicate the genome fraction (%Ref Aligned), calculated as the ratio of continuous aligned bases to the total reference genome length. Subplots above and beside each figure display histograms of the contig counts. Additionally, (E) shows the averaged genome fraction (%) of contigs from different long-read assembler pipelines. The complete data are available in Table S9.Figure S2. The average completeness of major HIV-1 open reading frames (ORFs) of the contigs generated from the assemblers analyzing FASTQ inputs of 4 median read lengths: (A) 1,000-nt, (B) 2,000-nt, (C) 3,000-nt, or (D) 4,000-nt.Figure S3. Contig size distribution of all assemblers processing the simulated FASTQ inputs of the 4 HIV-1 mixtures.Table S1. A list of experimental data and additional information. N/A: not applicable.Table S2. A statistical summary of runtime measurements taken from an assembly phase of the pipelines.Table S3. The memory usage and maximum CPU utilization of each assembler on three computational systems. The benchmark utilized 100 samples of two HIV-1 group M mixture with 2,000x coverage and 8,000-nt median read length.Table S4. The genome statistics of contigs generated from (A) Full genome laboratory isolate NL4-3, (B) Mpox propagated in a CV-1 cell line and (C) Mpox from pustular lesion, and (D) SARS-CoV-2 data by the selected assemblers.Table S5. The genome statistics of contigs generated from (A) Polio virus, (B) Hepatitis C virus (HCV), and (C) ZIKA Virus (ZIKV) data by the selected assemblers.Table S6. HIV Combinations for Data Simulation (Excel)Table S7. Characteristics of Simulated Samples Readlength Experiment (Excel)Table S8. Characteristics of Simulated Samples HIV mixture Experiment (Excel)Table S9. An Assembly Evaluation of HIV-1 Read Length Experiment (Excel)Table S10. An Assembly Evaluation of HIV-1 Subtype Mixtures Experiment (Excel)Table S11. Subtypes Recall Rates (Excel)Table S12. REGA Subtyping (Excel)Table S13. 5’ Half Genomes of NL4-3 Alignment Statistics (Excel)Table S14. Other Viruses Alignment Statistics (Excel)