16S / ITS amplicon
ASV-resolved profiling of bacterial, archaeal, or fungal communities from marker-gene surveys—higher resolution than legacy OTUs.
Core Bioinformatics
Metagenomics & Microbiome Analysis
From raw reads to a clear picture of a microbial community. We run 16S/ITS amplicon and shotgun metagenomics pipelines—profiling who is there and what they can do, assembling genomes, and testing what shifts between groups—and hand back tables and figures documented for publication and review.
FASTQ · 16S · shotgun in
Taxa · function · diversity out
Typical turnaround 3–7 days
Individual pricing from $149
Illustrative sample output
Firmicutes
Bacteroidetes
Proteobacteria
Overview
Rigorous microbiome analysis, without the in-house pipeline overhead
Metagenomics turns sequencing reads from a microbial community into a picture of its membership and function—which taxa are present, in what proportions, what they can do, and how that shifts between conditions. The hard part is rarely running a single tool; it is removing host and contaminant reads correctly, choosing amplicon or shotgun methods matched to your samples, handling compositional data with the right statistics, and documenting every decision so the result survives peer review.
We build and run that workflow for you. Whether you have a 16S amplicon survey of a hundred samples or shotgun data you want assembled into genomes, we take it through QC, profiling, diversity, and differential-abundance analysis using established, peer-reviewed tools—never opaque in-house black boxes—and return results with the tool versions and parameters recorded for full reproducibility.
Capabilities
What we analyse
One service spanning microbiome analysis end to end—from amplicon surveys to assembled genomes, taxonomy to function.
Shotgun taxonomic profiling
Species- and strain-level community composition from whole-metagenome reads, with relative-abundance estimation.
Functional & pathway profiling
Gene-family and pathway abundance from shotgun data to move beyond “who is there” to “what can they do.”
Assembly & binning (MAGs)
De novo assembly and genome binning to recover metagenome-assembled genomes, with completeness and contamination QC.
Diversity & differential abundance
Alpha- and beta-diversity, ordination, and compositional-aware tests for taxa that shift between groups.
AMR & virulence screening
Antimicrobial-resistance and virulence-gene profiling from reads or assemblies against curated reference databases.
Strain-level & comparative
Strain tracking, SNV-level resolution within species, and comparative genomics across recovered genomes.
Metatranscriptomics
Community gene expression to capture which functions are active—not just present—and how activity changes.
The Pipeline
How a microbiome analysis runs
A transparent, best-practice sequence—each step chosen for your data and question and documented in the final report. Nothing is a black box.
Steps are adapted to your design: 16S vs. shotgun, high- vs. low-biomass, profiling only vs. assembly and MAGs. We confirm the plan with you before any compute begins.
QC & host-read removal
Read QC, adapter and quality trimming, and removal of host and contaminant reads before profiling.
Tools: FastQC · MultiQC · fastp · KneadData
Denoising / read preparation
For amplicon: primer removal and ASV inference. For shotgun: quality-filtered reads ready for classification.
Tools: DADA2 · cutadapt · QIIME2
Taxonomic profiling
Taxonomy assigned against a curated reference—genus-level for amplicon, species and strain for shotgun.
Tools: QIIME2 · Kraken2 · Bracken · MetaPhlAn
Assembly & binning
For shotgun studies, de novo assembly and genome binning recover MAGs, with completeness and contamination checks.
Tools: MEGAHIT · MetaBAT2 · CheckM · GTDB-Tk
Functional profiling
Gene-family and pathway abundance, plus AMR and virulence screening where the study calls for it.
Tools: HUMAnN3 · eggNOG · CARD
Diversity & differential abundance
Alpha- and beta-diversity, ordination, and compositional-aware tests for taxa and functions that shift between groups.
Tools: phyloseq · vegan · ANCOM-BC · MaAsLin2
Reporting & delivery
Feature and taxonomy tables, publication-quality figures, a QC report, and reproducible methods with every tool version.
Tools: ggplot2 · MultiQC · versioned methods manifest
Tools & Technologies
Established, peer-reviewed tools—matched to your data
We select from the field's standard toolkit rather than forcing every dataset through one pipeline. A representative set of what we work with:
QC & host removal
FastQC
MultiQC
fastp
Trimmomatic
KneadData
Bowtie2
Amplicon (ASV / OTU)
QIIME2
DADA2
mothur
cutadapt
DECIPHER
Taxonomic profiling
Kraken2
Bracken
MetaPhlAn4
Centrifuge
Kaiju
mOTUs
Assembly & binning
MEGAHIT
metaSPAdes
MetaBAT2
MaxBin2
CONCOCT
DAS Tool
CheckM
GTDB-Tk
Functional & pathway
HUMAnN3
eggNOG-mapper
Prokka
KEGG
MetaCyc
Diversity & statistics
phyloseq
vegan
ANCOM-BC
LEfSe
MaAsLin2
AMR & virulence
CARD / RGI
ResFinder
AMRFinderPlus
abricate
VFDB
Visualization & review
ggplot2
Krona
iTOL
MultiQC
Reference Resources
Public knowledge behind every result
A profile is only as good as the reference behind it. We build on the community's authoritative, versioned databases.
- SILVA
- Curated ribosomal-RNA reference for 16S/18S taxonomic classification.
- Greengenes2
- Updated 16S reference tree and taxonomy for amplicon analysis.
- UNITE
- Reference database of fungal ITS sequences for mycobiome studies.
- GTDB
- Standardized, genome-based taxonomy for classifying MAGs and isolates.
- RefSeq / NCBI nt
- Comprehensive reference genomes and sequences for shotgun classification.
- KEGG
- Orthology and pathway maps for functional interpretation.
- MetaCyc
- Curated metabolic pathways underpinning HUMAnN functional profiles.
- CARD
- Comprehensive Antibiotic Resistance Database for AMR screening.
- VFDB
- Virulence-factor database for pathogenicity-gene profiling.
Choosing a Method
16S amplicon vs. shotgun vs. metatranscriptomics
There is no single best method—only the right one for your question, samples, and budget. A quick orientation; we will help you decide.
| Dimension | 16S / ITS amplicon | Shotgun metagenomics | Metatranscriptomics |
|---|---|---|---|
| Measures | Who is there (marker gene) | Who is there & what they can do | What the community is doing |
| Resolution | Genus, sometimes species | Species & strain level | Active genes & pathways |
| Functional info | Inferred only | Gene & pathway content | Expressed function |
| Relative cost | Lowest; robust to host DNA | Higher; more data & compute | Higher; RNA handling required |
| Best suited to | Large surveys, low-biomass samples | Function, strains, MAG recovery | Activity & regulation questions |
What You Receive
A complete, documented deliverable
Not just a feature table dropped in a folder—every output you need to interpret, publish, and reproduce the work.
- Feature table (ASV / OTU or taxonomic counts) with taxonomy
- Relative-abundance & taxonomy tables (TSV / BIOM)
- Alpha- & beta-diversity results with ordination
- Differential-abundance tables (ANCOM-BC / LEfSe / MaAsLin2)
- Functional / pathway profiles & AMR screening (shotgun)
- Assembled genomes (MAGs) with quality metrics, where applicable
- Publication-ready figures & methods with tool versions
Built for reproducibility, not just a result
Every pipeline follows documented best practices—correct host and contaminant removal, negative-control checks for low-biomass samples, and compositional-aware statistics—so differences between groups are real, not artifacts of uneven depth or contamination. We report read losses and rarefaction transparently. Each run records its tool versions, parameters, and reference database builds.
The practical payoff: your methods section writes itself, a reviewer can re-run the analysis, and a result from today can be reproduced a year from now. We will also tell you honestly when a design or sample size won't support the conclusion you're after.
FAQ
Metagenomics & microbiome questions
What researchers and project leads most often ask before starting a microbiome project.
16S (or ITS for fungi) is cost-effective and answers "who is there" at genus level from low-biomass or host-heavy samples. Shotgun sequencing resolves species and strains and adds functional and pathway content. We help you match the method to your question, budget, and sample type.
We start from raw reads (FASTQ) from your sequencing core — paired-end 16S/ITS amplicon or shotgun reads. If you have an existing feature or count table, we can pick up from there for diversity and differential-abundance analysis.
Yes. From shotgun data we profile gene families and pathways (HUMAnN, KEGG, MetaCyc), and can assemble and bin metagenome-assembled genomes (MAGs) with completeness and contamination assessment.
Yes. We remove host reads against the appropriate genome, apply decontamination and negative-control checks for low-biomass studies, and report the read losses transparently so the results are interpretable.
Yes. We screen reads or assemblies against curated databases such as CARD, ResFinder, and VFDB to profile antimicrobial-resistance and virulence-factor genes across your samples.
Feature and taxonomy tables, alpha- and beta-diversity with ordination, differential-abundance results (ANCOM-BC, LEfSe, or MaAsLin2), functional profiles where applicable, publication-quality figures, and reproducible methods with every tool version.
Related
Where microbiome work often leads next
Have microbiome data ready to analyse?
Tell us your organism, data type, and question—we'll scope it honestly, including if a different design would serve you better.