Table 1.
Online tools developed and the workflow process for which each would be used.
| Workflow | Tool Name | Description | Source | Input | Performance |
|---|---|---|---|---|---|
| Chromatograms | Quality Score Analyzer | Plots Chromatogram Quality Scores | Sanger | Chromatogram | 0.4 s for 1200 bases |
| Chromatograms | Automatic ContigGenerator Tool (ACGT) | Generates a contig from a forward and reverse chromatogram | Sanger | Chromatogram | 0.5 s for two chromatograms of 300 bases each |
| Alignment | Automatic Alignment Clean-up Tool (AACT) | Eliminates “gap-columns” and disambiguates ambiguous bases | Sanger NGS * | FASTA | 0.2 s for 3800 sequences of 3221 bases in length (12-MB file) |
| Alignment | Mind the Gap | Splits FASTA file based on gap threshold per column | Sanger NGS | FASTA | 0.5 s for 3800 sequences of 3221 bases in length (12-MB file) |
| Analysis | Babylon Translator | Extracts HBV protein sequences (ORFs) | Sanger NGS | FASTA | 0.9 s for 3800 sequences of 3221 bases in length (12-MB file) |
| Analysis | Wild-type 2 × 2 | Calculates 2 × 2 wild-type/mutant contingency tables | Sanger NGS | FASTA | 0.1 s for two groups of 50 sequences each of 3221 bases in length |
| Serotyping | HBV Serotype Tool | Determines HBV Serotype | Sanger NGS | FASTA FASTA |
0.6 s for 225 sequences of 3221 bases in length |
| Phylogenetics | Pipeline: TreeMail | Generates a phylogenetic tree | Sanger | Phylip | 1000 bootstraps of 41 sequences of 1000 bases required 15 min to process and email |
| GenBank Preparation | PadSeq Tool | Places two HBV sequence fragments on a template | Sanger | FASTA | 0.6 s to place 3800 sequences from each of two input files |
* Performance given in seconds (s), excluding network-dependent file uploading and page downloading times; NGS is next generation sequencing, such as ultra-deep pyrosequencing.