Metagenomics and microbiome analysis
Amplicon and shotgun microbiome data analyzed with compositional statistics, so a taxon that looks enriched really is enriched.
In short
OmicsQuest analyzes 16S rRNA, ITS and shotgun metagenomic sequencing, and metatranscriptomics. We infer amplicon sequence variants with DADA2, profile taxa and function with Kraken2/Bracken, MetaPhlAn and HUMAnN, assemble metagenome-assembled genomes, and test differential abundance with compositionally aware methods (ANCOM-BC2, MaAsLin2, ALDEx2). Pricing starts at $79/hour.
Publication-quality figures
The kind of multi-panel figure we deliver, styled to journal specifications and revised until it is right.
Metagenomics and microbiome: analyses we run
Every analysis below is available from raw data or from your processed files. Pick the ones your question needs; we recommend a robust core set during scoping.
Amplicon analysis
- ASV inference
- DADA2 denoising with chimera removal in QIIME 2.
- Taxonomic classification
- SILVA, GTDB or UNITE with naive Bayes classifiers.
- Contaminant removal
- decontam using negative controls and DNA concentration.
Shotgun metagenomics
- Taxonomic profiling
- Kraken2/Bracken and MetaPhlAn 4.
- Functional profiling
- HUMAnN pathways and gene families.
- Assembly and MAGs
- MEGAHIT/metaSPAdes, binning and CheckM2 quality.
- AMR and virulence genes
- CARD/RGI and VFDB screening.
Statistics
- Alpha and beta diversity
- Rarefaction-aware alpha diversity, PERMANOVA on appropriate distances.
- Compositional differential abundance
- ANCOM-BC2, MaAsLin2 and ALDEx2 consensus.
- Multi-omic integration
- Microbiome-metabolome and host transcriptome integration.
What you receive
- QC and contamination report
- Taxonomic and functional profiles
- Diversity and DA results
- Figures, code and methods
Mistakes our experts avoid
- Treating relative abundance as absoluteAn increase in one taxon forces apparent decreases in others. We use compositional methods.
- No negative controls in low-biomass samplesKit and reagent contaminants dominate low-biomass data. We remove them with controls.
Tools and methods
We choose methods for your design, benchmark where it matters, and document versions for reproducibility.
- QIIME 2
- DADA2
- Kraken2
- Bracken
- MetaPhlAn 4
- HUMAnN
- MEGAHIT
- CheckM2
- ANCOM-BC2
- MaAsLin2
- phyloseq
How a project runs
Scoping call
Thirty minutes, free. We learn the biology, the design and the deadline.
Capped estimate
A written plan with hours, deliverables and a cap. No surprise invoices.
Secure transfer and QC
Encrypted transfer, then a QC report and a go/no-go call within days.
Analysis with check-ins
Weekly calls with your duo team and interim figures you can steer.
Figures, methods, code
Publication-quality figures, methods text and reproducible code. Revisions are unlimited.
Frequently asked questions
16S or shotgun metagenomics?
16S is cheaper and good for community composition at genus level. Shotgun gives species and strain resolution plus functional potential. We can help you choose before sequencing.
Further reading
Send us your Metagenomics data question.
Send a few lines about your experiment. A bioinformatician and a biologist will review it and reply with questions or a capped estimate. Analysis starts at $79/hour, and figure customization is unlimited.
- Free 30-minute scoping call
- Capped estimate before any billable work
- You own all data, code, figures and IP
Prefer email? contact@omicsquest.com