Try two real genomes

These examples use public NCBI assemblies and the published database 2026-10-15. They show what the tool actually writes, including MLST alleles, a genomovar match and an unresolved species call.

Walk through the assigned genome · Walk through the unresolved genome

NCBI calls the first assembly E. hormaechei and the second Enterobacter sp. ECC-219. Pterobacter uses its documented taxonomic framework; the xiangfangensis subsp. hoffmannii combination is proposed. These are demonstrations, not an independent accuracy test. The first genome is itself a diversity reference and a member of the database’s GV10 definition.

Run them yourself

After installing Pterobacter, download and run the reproduction script. It requires Bash, curl, gzip and either sha256sum or shasum:

curl --fail --location \
  https://mbhall88.github.io/pterobacter/examples/public/reproduce.sh \
  --output reproduce.sh
bash reproduce.sh pterobacter-example

The script creates a new directory and refuses to overwrite an existing one. It downloads both whole assemblies, verifies their FASTA checksums, installs database version 2026-10-15 including MLST, and runs one assembly and a two-assembly batch. Allow roughly 1 GB for the database, inputs and results, plus alignment working space. Use local storage that supports the database installer’s atomic operations.

The classification commands inside that directory are:

ptero --database 2026-10-15 --database-dir ./database --threads 2 --sample-name RHBSTW-00333 \
  --anim-output single-alignments --output single.json --report-dir single \
  GCA_013738375.1.fna

ptero --database 2026-10-15 --database-dir ./database --threads 2 --jobs 1 --sample-sheet samples.tsv \
  --anim-output batch-alignments --output batch.json --report-dir batch

Both assemblies are supplied whole. RHBSTW-00333 has eight records, including its plasmids; ECC-219 has one chromosome record. MLST and ANIm are enabled by default. Only ECC-219 needs ANIm in these examples.

Inspect the saved outputs

The files are unedited outputs from source commit 0944f6d13b989f0329a6c266dbc9e20340fde58d, which reports software version 0.0.0 before the first release. Provenance records the source, database, input and output hashes. The checksums cover the saved reports and reproduction script.

For the exact implementation, build the source commit recorded above; later software versions may change results. Your local paths, process identifiers, timings, resource limits and software version will differ. Use the recorded assembly and database hashes when comparing results; byte-identical report files are not expected across machines. The saved reports retain the tool’s not_yet_validated metadata value; these examples do not change that status.

MLST uses PubMLST submissions through 31 December 2024. An ST describes an allele profile, not a species assignment: ECC-219 demonstrates that distinction. See MLST for scheme limits and genomovars for the scope of a GV match.