Fig. 1

Protocol schema and bioinformatics workflow. a Residual liquid-based cervical cytology collected for DNA extraction, PCR amplification of HPV DNA, and amplicon detection by capillary electrophoresis. Samples with + HPV DNA were sequenced by dideoxy (Sanger) and deep sequencing (Illumina®) methods for genotype identification. b Bioinformatics workflow created for next-generation sequencing (NGS) data and BLAST® search for HPV genotyping. Workflow layout in CLC Genomics Workbench consisting of 5 sequential steps: reads import, reads merging, reads QC, de novo assembly with mapping, and NCBI BLAST® search. c Representative read mapping result. Top to bottom: consensus sequence with nucleotide color space encoding (colored dots), coverage level (pink-bar height), and sequence reads (forward: green; reverse: red). d Representative nucleotide BLAST® result. The top sequence is the input (query) sequence, e.g., a consensus sequence derived from de novo assembly with nucleotide encoding (colored dots). Below, the matched (hit) sequences are displayed with nucleotide coloring and GenBank ID on the left. BLAST, Basic Local Alignment Search Tool; NCBI, National Center for Biotechnology Information; QC, Quality Control