Who's Inside
Every organism classified to species level. Relative abundance quantified for bacteria, archaea, fungi and viruses in one run.
Metagenomics Pipeline


Metagenomic samples are naturally messy. Host DNA, adapter contamination and duplicate reads corrupt everything downstream. We strip it all out before a single microbe gets classified.
Taxonomic classification names every organism. Abundance profiling counts them. Binning rebuilds their genomes. Functional annotation maps what each one is metabolically capable of.
Diversity reports, abundance profiles, MAG quality assessments and functional pathway maps all as interactive HTML reports delivered straight to your dashboard.
From raw FASTQ files to reconstructed genomes and pathway maps every deliverable you need to publish or present is in your dashboard the moment the run finishes.
Our Pipeline Modules
Every organism classified to species level. Relative abundance quantified for bacteria, archaea, fungi and viruses in one run.
Contigs binned by organism. Near-complete genomes assembled including species no lab has ever cultured before.
Genes, proteins and metabolic pathways annotated across the whole community. Know the functional potential of every organism.
GenomeBeans handles taxonomy MAGs and pathway analysis automatically and delivers them as interactive visual reports the moment your run finishes.
Regular genomics studies one organism at a time. Metagenomics sequences everything in a sample at once including bacteria, viruses, fungi and archaea without culturing them. One run gives you the full picture of an entire microbial ecosystem.
A Metagenome-Assembled Genome is a near-complete genome rebuilt from a complex microbial mixture without isolating the organism. Binning groups reads by organism and reconstructs the genome. This lets you study species no one has ever grown in a lab including entirely new ones your sample might contain.
16S targets a single marker gene fast and cheap but only identifies bacteria and misses viruses, fungi and archaea entirely. Shotgun metagenomics sequences everything across all kingdoms plus functional genes and metabolic pathways. GenomeBeans uses shotgun for the complete picture.
Three interactive reports a taxonomic diversity report with abundance profiles and phylogenetic trees, a MAG quality summary with completeness and contamination scores, and a functional pathway report with KEGG, COG and GO annotations. All shareable HTML delivered to your dashboard.
Most runs complete within a few hours depending on dataset size. GenomeBeans processes everything in parallel from QC to annotation so you don’t wait for step-by-step outputs. You get the full interactive report the moment analysis finishes.
100% private. You own everything you upload. Never shared. Never sold. Results archived for 90 days then permanently deleted. No exceptions. No fine print.
