Bacterial WGS
Paired-read QC, preprocessing, assembly and annotation.
Read methodsRESEARCH RESOURCES
Scientific Methods
How AstroNexus analyses are performed, what outputs mean, and the limits of computational interpretation.
Pairwise comparison
ANI, assembly statistics and annotated protein comparison.
Read methodsMulti-genome comparison
Gene-family presence/absence across a collection of assemblies.
Read methodsTargeted comparison
Exact annotated gene-name or locus-tag matches across assemblies.
Read methodsValidated tool versions
The versions below are recorded in validated WGS and Comparative outputs. Installed software and the tools actually used are different concepts; consult the per-analysis version record.
| Tool | Role | Recorded version |
|---|---|---|
| FastQC | Read QC | 0.12.1 |
| fastp | Default read preprocessing | 1.1.0 |
| MultiQC | QC aggregation | 1.35 |
| SPAdes | WGS assembly | 4.3.0 |
| QUAST | Assembly assessment | 5.3.0 |
| Bakta | WGS / Pairwise annotation | 1.11.4 |
| Nextflow | WGS orchestration | 26.04.6 |
| FastANI | Pairwise ANI | 1.34 |
| BLASTP | Pairwise protein comparison | 2.16.0+ |
| Prokka | Multi-genome / Targeted annotation | 1.15.6 |
| Panaroo | Multi-genome family clustering | 1.6.0 |
Workflow records & reproducibility
This documentation was checked against the recovery-hardened release (a63799e, 4 October 2026). WGS reports record pipeline version 2.0.0; Comparative outputs record pairwise-1.0, multigenome-1.0 or targeted-1.0 and their source commit.
Use the report, methods/tool-version files, result manifest and checksums to identify an analysis and verify delivered files. These records support traceability; they do not guarantee bit-for-bit reproduction on a different machine or database. Database versions are stated only where recorded.
How to cite AstroNexus
No AstroNexus journal article or DOI is asserted here. A platform citation can use the following format; replace the access date and state the analysis type and recorded workflow/tool versions in your Methods section.
AstroNexus Bioinformatics. AstroNexus bacterial genomics analysis platform. https://savage-wgs-report.web.app/portal/. Accessed [day month year].
Also cite the original software used in your analysis, following the citation guidance supplied by each software project. Tool documentation links below help locate the relevant guidance; they are not an AstroNexus publication.
Research use only. Not for clinical or diagnostic use.