User guide
Start with a whole isolate assembly in FASTA format. Pterobacter keeps all supplied records, including plasmids and short contigs, and reports the most specific supported call with its reasons.
| Task | Guide |
|---|---|
| Install from the private source | Installation |
| Install and verify managed components | Database management |
| Verify explicit reference paths | Reference setup |
| Analyse one assembly or a batch | Running Pterobacter |
| Find the answer and warnings | Reading results |
| Investigate an uncertain result | Boundary review and worked example |
| Check which taxa are represented | Reference coverage |
| Understand sequence typing | MLST |
| Interpret a genomovar match | Genomovar matches |
| Resolve a failed run | Troubleshooting |
Use one isolate assembly per input. Reads, metagenomes and mixed samples are outside the supported input. Query quality control is your responsibility; the program does not run CheckM2 and a completed report does not certify purity.
The full command-line help lists all options exactly as ptero --help prints them.
The report reference describes every output field and includes a separate illustrative manual-review recipe. The command reference covers advanced ANIm settings, cache verification and exit codes. The published reference database can be installed with ptero database install 2026-10-15.