Bacterial Genomics · Hybrid & Long-Read Assembly

Complete, closed, annotated.

Most bacterial genomes can now be assembled into complete, closed chromosomes with plasmids — not drafts with hundreds of contigs. Nucleome Informatics offers short-read, long-read, and hybrid workflows matched to your question: outbreak tracing needs speed and accuracy; novel isolates need completeness; AMR surveillance needs plasmid linkage.

Plan Your Project → Learn the Basics
Closed genomes
— chromosome + plasmids
Hybrid assembly
Illumina + ONT/PacBio
AMR, virulence & MLST
profiling
Pan-genome & phylogenomics
About the Service

Bacterial Genome Sequencing at Nucleome Informatics

Bacterial genomes are small (typically 0.5–10 Mb), haploid, and — with long reads — fully assemblable. Nucleome Informatics offers three workflow tiers:

  • Assembly (contigs or closed chromosome + plasmids, per workflow) with QC metrics (N50, completeness, CheckM/CheckM2 contamination)
  • Annotation (Prokka/Bakta): coding sequences, RNAs, functional assignment
  • Typing: MLST, serotyping (where applicable), species confirmation (ANI against reference databases)
  • AMR gene and virulence factor detection (AMRFinderPlus, ResFinder, CARD/RGI; VFDB)
  • Plasmid identification and reconstruction (MOB-suite, PlasmidFinder)
  • Phylogenetics: core-genome SNP trees, pan-genome analysis (Panaroo/Roary), recombination screening (Gubbins)

Why complete genomes matter

  • Plasmids resolved: short reads cannot separate plasmid from chromosome repeats; long reads reconstruct plasmids as complete circles — including which AMR genes ride on which plasmid.
  • No assembly blind spots: rRNA operons, IS elements, and phase-variable tracts assemble correctly.
  • Reference quality: a closed genome is a durable community resource and the basis for all downstream comparisons.
Learning Path

From first principles to expert-level analysis

New here? Start with Foundations. Planning a study or reviewing results? Jump to Practitioner or Expert. Each level builds on the one before it, so you can read this page as a short course or dip in where you need to.

Start here if you are new to this service — six ideas that explain what it is and why it matters.

LEVEL 1

What is a bacterial genome assembly?

The reconstructed DNA sequence of a bacterium's chromosome (and plasmids), built from sequencing reads. A "closed" genome is one continuous chromosome sequence with no gaps.

LEVEL 1

Draft vs complete assembly

Draft assemblies (short reads) break into tens–hundreds of contigs at repeats. Complete assemblies (long reads) recover the chromosome as one piece plus circular plasmids.

LEVEL 1

What is hybrid assembly?

Combining long reads (structure) with short reads (accuracy) — the standard recipe for finished bacterial genomes.

LEVEL 1

What is MLST?

Multi-locus sequence typing: classifying isolates by alleles at a fixed set of housekeeping genes — the shared language of bacterial epidemiology.

LEVEL 1

What is ANI?

Average nucleotide identity — the similarity measure used to confirm species boundaries (>~95% ANI ≈ same species).

LEVEL 1

What samples do I send?

Purified DNA or a live isolate (streaked culture). We provide submission guidance; DNA quantity requirements are modest for bacteria.

For scientists planning a project or reading a report: how each step works and how it can mislead.

LEVEL 2

Workflow selection

Short-read-only for large collections and SNP-based epidemiology; long-read or hybrid for complete genomes, plasmid reconstruction, and novel species. We recommend per project.

LEVEL 2

Library and sequencing

Illumina paired-end (150–250 bp) for accuracy; ONT rapid-barcode or ligation libraries (or PacBio HiFi libraries) for structure. Bacterial genomes need modest data volumes — projects are fast and economical.

LEVEL 2

Assembly and QC

Unicycler/hifiasm/trycycler-style assembly; completeness and contamination via CheckM; circularity verified by read coverage across the join; plasmids reconstructed and named.

LEVEL 2

Annotation

Prokka or Bakta: gene calling, RNA features, functional annotation, and standard output formats for downstream tools and NCBI submission.

LEVEL 2

AMR and virulence

AMR genes detected against curated databases with long-read linkage to plasmid or chromosome — critical for interpreting horizontal transfer risk.

LEVEL 2

Phylogenetics and pan-genomics

Core-SNP alignment, recombination filtering, and maximum-likelihood trees; pan-genome analysis for gene gain/loss across collections.

For study design: the decisions that determine whether the data answers your question.

LEVEL 3

Outbreak and surveillance design

For outbreak tracing, short-read SNP phylogenetics with recombination filtering is the standard; include the suspected source/ancestral isolates and sequence at consistent depth.

LEVEL 3

Novel species and taxonomy

Complete genomes plus ANI, dDDH estimates, and annotation support formal species description; we format assemblies for NCBI submission (including complete-genome tracks).

LEVEL 3

AMR surveillance programmes

Long-read linkage of AMR genes to plasmids enables horizontal-transfer risk assessment — the question surveillance programmes actually need answered.

LEVEL 3

Comparative and evolutionary genomics

Pan-genome dynamics, gene gain/loss dating, and selective-pressure analysis (dN/dS) across collections; we support the full comparative toolkit.

LEVEL 3

Methylation and epigenetics

ONT and PacBio reads detect bacterial methylation motifs directly — relevant to phase variation and restriction–modification biology.

LEVEL 3

Reporting standards

We follow MIGS/MIxS norms: assembly methods, versions, coverage, and QC metrics documented for every genome.

Closed genome
a complete, gapless chromosome assembly.
Plasmid reconstruction
assembling plasmids as complete circular sequences.
ANI
average nucleotide identity; species-delimitation metric.
Pan-genome
the union of gene families across a collection of isolates.
IS element
insertion sequence; a small transposable element that complicates assembly.
GQN/CheckM
genome quality/completeness estimation from marker genes.
The Science

How it works, in two figures

Hybrid assembly with Unicycler and long-read-only assembly with hifiasm/trycycler workflows are established in the bacterial genomics literature; AMR detection standards come from CARD/AMRFinderPlus curation. See references below.

Figure 1 Draft vs closed assembly. schematic
Draft assembly (short reads) Closed genome (long reads) Tens–hundreds of contigs Plasmids fragmented at repeats rRNA operons collapsed Chromosome + plasmids as circles AMR genes linked to plasmids NCBI-ready complete genome
Figure 1 | Draft vs closed assembly. (Illustrative schematic, not sample data.)
Figure 2 Workflow. schematic
Isolate / DNA Illumina + ONT / PacBio Hybrid assembly (Unicycler) Polishing & circularity check Annotation + AMR / MLST Phylogenomics & NCBI files
Figure 2 | Workflow. (Illustrative schematic, not sample data.)
Technology Highlights

Built for the questions you are asking

The platforms, pipelines and standards behind this service.

Illumina short-read accuracy

≥99.9% base accuracy for variant-level comparisons, outbreak SNP calling, and large collections at economical per-sample cost.

Oxford Nanopore PromethION

Reads longer than most bacterial genomes resolve chromosomes and plasmids as complete circles; rapid workflows support time-critical outbreak work.

PacBio HiFi

≥99.9% accurate long reads — the highest-quality single-technology bacterial assembly available.

Hybrid assembly pipelines

Unicycler-style hybrid assembly (long-read scaffold, short-read polish) delivers closed, polished genomes — the reference standard.

AMR and virulence profiling

Detection against CARD, ResFinder, AMRFinderPlus, and VFDB, with plasmid/chromosome linkage from long reads.

Pan-genome and phylogenomics

Panaroo/Roary pan-genomes, core-SNP phylogenies, recombination filtering (Gubbins), and MLST/serotype calling for epidemiological context. ---

Scope Note

What this service does and does not cover

Scope note. Complete, closed assemblies are achievable for the large majority of bacterial isolates but depend on DNA quality and genome architecture (very high IS-element burdens or extreme plasmid diversity can complicate closure; we report per-replicon status honestly). Mixed cultures and metagenome-derived bins are different workflows (see our Shotgun Metagenomics page). AMR phenotype prediction from genotype is probabilistic — genotype is reported; phenotype confirmation remains the laboratory's role. ---
Why Nucleome

Service highlights

What you can expect from our team in Hyderabad.

All three workflow tiers

Short-read, long-read, and hybrid — matched to your question and budget.

Closed genomes as standard

Chromosome + plasmids, circularity-verified, NCBI-ready.

AMR with plasmid linkage

Not just which genes — where they live.

Fast turnaround potential

Bacterial projects are small-data and quick; timelines agreed per project.

Epidemiology-ready outputs

MLST, core-SNP trees, pan-genomes — publication and surveillance ready.

India-relevant collections

Experience with clinical, environmental, food, and agricultural isolates from Indian programmes. ---

Questions

Frequently asked, in plain language

From the basics to the finer points of design and interpretation.

basicCan you give me a complete genome with plasmids?
Yes — with long-read or hybrid sequencing, most bacterial isolates assemble into a closed chromosome plus circular plasmids.
basicHow much DNA do you need?
Bacterial projects need modest DNA quantities; we provide exact submission guidance at intake.
basicDo you identify the species?
Yes — ANI-based species confirmation and MLST are included in every report.
intermediateShort reads or long reads for my project?
Large collections and SNP-based epidemiology: short reads. Complete genomes, plasmids, novel species: long reads or hybrid. We recommend per project.
intermediateCan you tell which plasmid carries an AMR gene?
Yes — that linkage is one of the core advantages of long-read bacterial sequencing.
intermediateDo you provide annotation?
Yes — Prokka/Bakta annotation with gene calls, RNAs, and functional assignment, in standard formats.
advancedCan you support a novel species description?
Yes — complete genome, ANI/dDDH estimates, annotation, and NCBI submission formatting.
advancedCan you do pan-genome analysis across my collection?
Yes — Panaroo/Roary pan-genomes, core-SNP phylogenies with recombination filtering, and gene gain/loss analysis.
advancedCan methylation motifs be detected?
Yes — native long reads (ONT and PacBio) detect bacterial methylation motifs directly; discuss at project design.
advancedIs AMR phenotype predicted?
Genotype is reported against curated databases; phenotype prediction is probabilistic and flagged as such — phenotype confirmation remains with the microbiology laboratory.
References

Key literature & resources

Selected sources behind the methods and reference values on this page. Figures labelled "schematic" or "illustrative" are generated for this page, not client data.

  1. Wick RR, et al. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Computational Biology. 2017;13(6):e1005595.
  2. Cheng H, et al. Haplotype-resolved de novo assembly with phased assembly graphs (hifiasm). Nature Methods. 2021;18(2):170–175.
  3. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. (Bakta: Schwengers O, et al. Microbial Genomics. 2021;7(11).)
  4. Chklovski A, et al. CheckM2 — improved assessment of genomic completeness and contamination. Nature Biotechnology. 2023;41(12):1633–1638.
  5. Alcock BP, et al. CARD 2023: expanded curation, support for machine learning, and metadata. Nucleic Acids Research. 2023;51(D1):D690–D709.
  6. Feldgarden M, et al. AMRFinderPlus 2023 Release. Nucleic Acids Research. 2023 (AMRFinderPlus database updates).
  7. Tonkin-Hill G, et al. Producing bacterial pangenomes with Panaroo. Nature Communications. 2020;11(1):5705.
  8. Croucher NJ, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research. 2015;43(3):e15.