Bacterial whole-genome analysis.
The bacterialp pipeline takes raw Oxford Nanopore FASTQ files and produces a single self-contained HTML report — species identification, assembly, AMR profile, MLST, and species-specific typing in one document.
Designed for clinical and public-health microbiology workflows where turnaround time and traceability matter. The final report can be opened in any browser, saved as PDF, or archived into a patient record.
Six worked examples from public Nanopore data.
Click any card to open the full interactive report — exactly what you receive.
Eight stages, fully automated.click any stage for tools
From quality filtering to species-specific typing — every stage runs without manual intervention, with full provenance captured for the audit trail.
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01 Quality filtering
Trims sequencing adapters, removes low-quality bases, and discards reads that fall below length or quality thresholds — clean input for everything downstream.
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02 Taxonomic classification
Identifies the species in the sample by matching k-mers against a curated reference database. Confirms the expected organism and flags contamination early.
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03 De novo assembly
Reconstructs the bacterial genome from filtered long reads, including chromosomal and plasmid contigs. Optimised for Nanopore-only or hybrid input.
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04 Genome completeness
Scores the assembly against expected single-copy orthologs to measure completeness, duplication, and fragmentation. Surfaces incomplete or fragmented assemblies before they reach the report.
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05 Gene annotation
Predicts and labels coding sequences, rRNA, tRNA, and other genomic features. Produces a structured annotation suitable for downstream comparative work.
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06 AMR detection
Screens the assembly for known antimicrobial resistance genes and assesses plasmid context — with resistance class, coverage, and identity reported per hit.
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07 MLST typing
Assigns a sequence type by matching the canonical seven housekeeping gene alleles to PubMLST schemes — the standard genotyping framework for epidemiology.
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08 Species-specific typing
When Kraken2 identifies a clinically-relevant species, the pipeline automatically branches into the appropriate typing tool — serotyping, capsule typing, SCCmec, and more. See the cards below for the full set.
Auto-selected per species
Species-specific typing tools.
When a known clinically-relevant species is identified, the pipeline automatically runs the appropriate typing tool for that organism.
What the report includes.
Eight sections, all in one HTML file. Interactive charts, sortable tables, and CSV exports throughout.
16S / ITS amplicon analysis.
The NS Amplicon pipeline profiles mixed microbial communities from Oxford Nanopore 16S rRNA or ITS sequencing — what is in the sample, and in what proportions?
Raw FASTQ files are taken through quality filtering, read clustering, consensus polishing, and taxonomic classification to produce per-sample abundance reports with diversity metrics and rarefaction curves.
WGS asks what is this isolate? — deep, strain-level resolution from a single cultured organism.
Amplicon sequencing asks what is in this mixed community, and at what relative abundance? — no culture needed, but genus-level resolution.
Worked example: gut mock community.
A 12-species mock community sequenced on Nanopore. Click to open the full report — exactly what you receive.
Six stages, optimised for Nanopore amplicons.click any stage for tools
From raw long reads to polished consensus sequences and diversity metrics — tuned for the error profile of Oxford Nanopore amplicon data.
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01 Quality filtering
Trims adapters and length-filters reads to within the expected amplicon size window, removing chimeras and off-target sequences.
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04 Taxonomic classification
Aligns each polished consensus against SILVA (16S) or UNITE (ITS) reference databases to assign taxonomy to the lowest reliable rank.
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05 Abundance estimation
Resolves multi-mapped reads to fractional taxon abundances using expectation-maximisation — producing accurate proportions even with closely-related taxa.
Expectation-Maximisation -
06 Diversity & rarefaction
Calculates Shannon and Simpson diversity indices and produces rarefaction curves to assess whether sequencing depth captured the full community.
Shannon (H′) Simpson (1−D) Rarefaction
Diversity metrics, briefly explained.
Three standard ecological measures, reported per sample, that together describe community structure.
What the report includes.
All processing on sovereign UK infrastructure.
Sequencing data never leaves NS Bio's self-hosted environment. Reports are self-contained HTML files with no CDN requests, no analytics, and no third-party fonts loaded at runtime — every asset is embedded directly in the file. A report opened offline in five years' time will render exactly as it did on the day it was delivered.
Want to run one of these on your data?
Initial conversations are free and confidential. We'll discuss your sample type, sequencing platform, and turnaround — followed by a written quote within a week.