User Guide
Graphical Abstract
（I）ANALYSIS
Upload complete or draft genome files
Search results for an existing job
（II）RESULTS
Uploaded Files List
Species identification
Summary
Annotation
Circos plot
Potential risk score
Antimicrobial resistance gene
Virulence factor
Pathogenic genes
Plasmid
Prophage
Insertion Sequence
KEGG Pathway
KEGG Functional Category
COGs
CAZy
antiSMASH
gutSMASH
（III）Uploaded strains comparison
Comparative analysis of uploaded strains
ANI
Potential risk score
Antimicrobial resistance gene
Virulence factor
Pathogenic genes
Plasmid
COGs
CAZy
KEGG Pathway
KEGG Functional Category
Ortholog Comparison
UBCG analysis
cgMLST analysis
UBCG v.s. cgMLST
（IV）List of software and databases used in BacGenAnalytica
| Function | Software | Database |
|---|---|---|
| Genome identification | ||
| Type strains comparison | Mash v2.3 | NCBI prokaryote type strains (Aug. 2023 release) |
| Average nucleotide identity (ANI) | https://github.com/chjp/ANI | － |
| Genome Circos plot | mummer2circos v1.4.2 | － |
| Circos v0.69-8 | － | |
| Genome Annotation | eggNOG-mapper v2.1.12 | eggNOG v5.0.2 (Mar. 2021 release) |
| Safety analysis | ||
| Antibiotic resistance genes (ARGs) | RGI v6.0.3 (BLAST homolog detection) | CARD Variants v4.0.2 (Nov. 2023 release) |
| ResFinder v4.6.0 | resfinder_db (Aug. 2024 release) | |
| AMRFinderPlus v4.0.3 | (Oct. 2024 release) | |
| Virulence factors (VFs) | BLASTN v2.16.0 | VFDB (Dec. 2024 release) |
| VirulenceFinder v2.0.4 | virulencefinder_db (Feb . 2024 release) | |
| Pathogenic genes (PGs) | BLASTX v2.16.0 | PHI-base v4.16 (May. 2024 release) |
| Plasmid genes | PlasmidFinder v2.1.6 | plasmidfinder_db v2.2.0 (Nov. 2024 release) |
| PlasmidHunter v1.4.5 | (May. 2024 release) | |
| Prophage regions | Phigaro v2.4.0 | (Jan. 2024 release) |
| Insertion Sequence | ISEScan v1.7.2.3 | (Apr. 2021 release) |
| Functional analysis | ||
| Secondary metabolite gene clusters | antiSMASH v7.1.0 | (Nov. 2023 release) |
| Primary metabolite gene clusters | gutSMASH v1.0.0 | (Oct. 2020 release) |
| Phylogenetic analysis | ||
| 81 core gene-based phylogeny | UBCG2 | ubcg_v2.hmm (2021 release) |
| cgMLST phylogeny | PGAdb-builder | － |
（V）Browser compatibility
| OS | Version | Chrome | Firefox | Microsoft Edge | Safari |
|---|---|---|---|---|---|
| Linux | CentOS 7 | not tested | 61.0 | n/a | n/a |
| MacOS | Big Sur, High Sierra | 96.0.4664.110 | 61.0 | n/a | 14.1.1, 13.1.2 |
| Windows | 10 | 96.0.4664.110 | 61.0 | 42.17134.1.0 | n/a |