Microbial & bacterial genomics
Microbial Genomics Bioinformatics Services: Assembly, Annotation and Comparative Analysis
We analyze existing Illumina, Oxford Nanopore and PacBio data, from raw FASTQ files to assembled genomes, to deliver publication-ready bacterial genome assemblies, annotations and comparative-genomics results.
For bacterial and archaeal genomes, with methods adapted to your organism, sequencing platform and research question. Analysis of existing data; sequencing is arranged separately.
Analysis capabilities
Our Microbial Bioinformatics Services
Start from raw reads or existing assemblies. The analyses are agreed around your project; not every project needs every step.
Quality assessment & preprocessing
Evaluate raw sequencing data, inspect read quality and assess potential contamination. Depending on the platform, preprocessing may use FastQC, fastp or Trimmomatic. Quality limitations are reported rather than hidden by filtering.
Taxonomic assignment & phylogenomics
Assess genomic relatedness using ANI and dDDH where appropriate, and infer phylogenetic relationships using suitable marker or genome-based methods. Approaches may include TYGS, OrthoANI and 16S rRNA analysis. ANI measures similarity; it is not itself a phylogenetic tree.
Project-adapted workflows & consulting
Combine established methods, adjust tools and parameters, and define suitable comparisons for your research question. We can discuss unusual organisms, existing assemblies, non-standard inputs and optional multi-omics integration before agreeing the work.
Research outcomes
What can you achieve with our microbial genomics services?
Identify and compare strains
Assess species placement and relationships among isolates, and investigate shared or distinctive genomic features.
Explore metabolic potential
Investigate biosynthetic and catabolic pathways, functional domains and candidate genes relevant to ecological roles or biotechnology.
Interpret resistance and virulence features
Screen for known antibiotic resistance genes and virulence-associated features where included. Genomic predictions need to be interpreted in their biological context.
Communicate the results
Receive interpretable genome statistics, annotation tables, comparative figures and reporting suited to your research question.
Analytical workflow
A typical microbial genomics analysis workflow
The path depends on your starting data and agreed scope. Existing assemblies can enter at quality assessment and annotation. Direct communication continues throughout the project.
01 · Quality control
Read quality, adapters and potential contaminants
View step details
For bacterial isolate reads, inspect quality and sample consistency before choosing filtering or trimming steps.
02 · Genome assembly
Short-read, long-read or hybrid assembly
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Assemble each isolate and assess contiguity and quality. Select polishing where appropriate; report unresolved regions or limitations.
03 · Genome annotation
Genes, RNAs and functional potential
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Annotate assemblies consistently so gene-content comparisons are meaningful; add functional or resistance screening when included.
04 · Comparative genomics
Relatedness, pan-genome and phylogeny
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Use appropriate reference genomes and methods to compare ANI, core/accessory genes and phylogenomic relationships.
05 · Reporting & visualization
Files, figures, tables and interpretation
View step details
Summarize the agreed analyses, document methods and limitations, and discuss the biological findings.
What you receive
Deliverables — files you can use
The quotation specifies your deliverables. The list below describes available outputs, rather than a promise that every project includes every analysis.
Genome assemblies
FASTA assemblies, assembly statistics and quality assessments. Polished or circularized versions are supplied where supported by the data and included in scope.
Annotated genomes
GFF, GBK and tabular annotation files, including coding sequences, tRNAs, rRNAs and functional assignments as applicable.
Comparative-genomics outputs
Core/pan-genome matrices, shared and unique gene tables, and suitable heatmaps, Venn diagrams or synteny plots where included.
Summary report and optional processed reads
A PDF report describing methods, summary statistics, key findings and interpretation. Quality-filtered FASTQ files and return copies of the supplied raw reads can be agreed when needed.
Scientific experience
Why choose Tailoredomics?
Analysis grounded in the organism and experiment
Experience with pathogens, symbionts, extremophiles and environmental isolates informs the choice of methods and interpretation. Bacteria and archaea are the main focus; microbial eukaryote projects can be assessed according to the organism and required analysis.
We select established tools and appropriate versions for the project, document methods and limitations, and discuss the results directly. Optional transcriptomics, proteomics or metagenomics integration can be scoped where useful.
Published research · BMC Genomics
Comparative genomics of Fervidobacterium
Research combining genome assembly, annotation, ANI, pan-genome analysis and genome-based phylogeny demonstrates methods relevant to this service.
View the research publication →
Research evidence, rather than a claim that the study was a commercial client project.
Research contexts
Applications of microbial genomics
Environmental & agricultural microbiology
Investigate isolates from soil, water, plant-associated systems and extreme environments, including candidate functions relevant to nutrient cycling or biodegradation. For community-level questions, see our microbiome data analysis services.
Biotechnology & synthetic biology
Explore metabolic pathways and gene clusters to prioritize candidates for enzyme discovery, biosynthesis studies or microbial engineering.
Resistance research
Investigate resistance genes and mobile genetic elements across isolates to support antimicrobial resistance research and surveillance questions. Sequence findings alone do not establish susceptibility.
Evolution, taxonomy & novel species
Study gene gain/loss and genome organization, and use genome-based comparisons to support taxonomic placement and investigation of potential novel taxa.
Before you enquire
Frequently asked questions
What types of microorganisms can you analyze?
Our main focus is bacteria and archaea, including environmental isolates, pathogens, symbionts and industrial strains. Tell us about microbial eukaryotes so we can assess the appropriate methods and scope. Mixed-community sequencing may require a metagenomics or microbiome workflow.
What data formats do you accept?
We accept raw sequencing reads in FASTQ format from Illumina, Oxford Nanopore and PacBio, including hybrid datasets. Existing assemblies in FASTA format can be assessed for annotation and downstream analysis.
Can you work with assemblies I already have?
Yes. We can begin with assembly assessment, annotation, taxonomic assignment or comparative genomics, depending on the files available and your research question.
Can you guarantee a complete bacterial genome?
Genome closure depends on the sequencing data, coverage, repeat structure and sample quality. We assess the available data and report assembly quality and limitations; a complete or circularized genome is not guaranteed in advance.
How long will the analysis take, and how much will it cost?
Timing and cost depend on the number of samples, data volume, starting files and analyses requested. We agree the scope, deliverables, price and schedule before work begins.
How do I send my sequencing data?
Start with a description of your project; there is no need to upload raw data in the enquiry form. We then agree a transfer method, such as a sequencing-provider or institutional download link.
Can I request particular tools or additional analyses?
Tell us about required tools, reference datasets or existing workflows when discussing the project. We assess their suitability and agree any additional analyses and deliverables before including them.
Background reading
What is microbial & bacterial genomics?
Microbial genomics studies the genomes of microorganisms; bacterial genomics focuses on bacteria. Genome analysis can support taxonomic classification, functional prediction and comparative microbial genomics.
For the longer introduction, read What is Microbial Genomics?
Discuss your project
Ready to get started?
Tell us about your organism, sequencing data, number of samples and the questions you want to answer. We can then define the analysis and quotation.
Request a quoteEmail info@tailoredomics.com
No raw-data upload is needed at first contact.