A targeted sequencing approach that focuses on specific genetic regions of interest. Think of it as using a spotlight to examine particular areas rather than scanning an entire room. Amplicon sequencing uses primers (short DNA sequences) to amplify and sequence specific genes, making it ideal for identifying and quantifying organisms in a sample quickly and cost-effectively. 

When to use it: Biodiversity studies, monitoring specific microbial groups, high-throughput screening. 

Sequencing all the genetic material present in an environmental sample without targeting specific regions. Unlike amplicon sequencing, this captures everything—providing a complete picture of who’s there and what they can do. It’s like reading every book in a library instead of just the titles. 

When to use it: Discovering unknown organisms, understanding microbial functions, comprehensive community analysis. 

Sequencing the complete genetic blueprint of a single organism. This provides detailed information about one specific bacterium or microbe, including all its genes and capabilities. 

When to use it: Characterizing specific strains, quality control, understanding particular organisms in detail. 

The total amount of genetic information sequenced from your sample, typically measured in basepairs or gigabasepairs. Greater depth allows you to detect rare organisms and genes that might be missed with shallow sequencing.

Example: 10 Gigabasepairs means 10 billion DNA letters were sequenced from your sample.

Yes. GeneDance specializes in environmental microbiome analysis across multiple industries including wastewater treatment, soil health assessment, fermentation process optimization, food safety testing, and bioremediation monitoring. Our analysis pipelines are optimized for these applications and include industry-specific reporting formats for compliance and quality assurance.

Sequencing both ends of a DNA fragment, providing more information than reading just one end. This helps assemble sequences more accurately and identifies how genes are organized. Think of it as reading both the beginning and end of a sentence to better understand its meaning. 

A laboratory technique that measures the precise amount of specific DNA sequences in your sample. While sequencing tells you what’s present, qPCR tells you exactly how much. It’s highly sensitive and can detect even small amounts of target genes. 

When to use it: Validating sequencing results, quantifying specific organisms or genes, monitoring changes over time. 

Short DNA sequences that act as starting points for amplification and sequencing. Pre-tested primers target well-known genes (like the 16S gene for bacteria), while custom primers can target any genetic region you specify. 

The application of computational tools to analyze biological data. In microbiome research, this means converting raw sequencing data into meaningful biological insights—identifying species, predicting functions, and answering your research questions. 

The first step in data processing where low-quality data, errors, and artifacts from the sequencing machine are removed. This ensures you’re working with accurate, reliable data. 

Piecing together short DNA sequences (reads) into longer, continuous sequences, similar to assembling a puzzle. This is particularly important for genome sequencing where you want to reconstruct complete genetic blueprints. 

Adding biological meaning to DNA sequences by identifying genes, their functions, and other genetic features. It’s like adding labels to a map—turning raw sequence data into interpretable information. 

Functional annotation: Identifying what genes do (their biological functions). 

Taxonomic annotation: Identifying which organisms the genes come from. 

Sorting mixed DNA sequences from a metagenomic sample into groups that likely belong to the same organism. This allows you to reconstruct individual genomes from complex environmental samples containing hundreds of species. 

Assessing the variety and abundance of different organisms in your sample. This includes both species richness (how many different types) and evenness (how their abundances compare). 

Describing the composition and structure of a microbial community—who’s present, how abundant they are, and how they relate to each other. 

Determining which organisms are present in your sample by comparing their genetic sequences to reference databases of known species. Each organism has unique genetic signatures that serve as molecular fingerprints. 

Inferring the biochemical capabilities of organisms in your sample by identifying genes involved in specific metabolic processes. This reveals what the community can do—produce vitamins, break down pollutants, cycle nutrients, etc. 

Genes that allow bacteria to survive antibiotic treatment. Detecting these genes helps assess health risks and track the spread of antibiotic resistance in environmental and clinical samples. 

Genes that enable pathogens to cause disease, such as toxins or mechanisms for invading host cells. Identifying these helps assess potential health hazards in your samples. 

Biochemical pathways that produce specialized compounds not essential for basic survival, such as antibiotics, pigments, or signaling molecules. These often have biotechnological or pharmaceutical applications. 

The collective enzyme functions present in a microbial community, revealing what biochemical transformations the community can perform—decomposing organic matter, synthesizing compounds, or modifying their environment. 

DNA sequences that can move between different locations in genomes or between organisms, often carrying resistance or virulence genes. Understanding these helps track how traits spread through microbial communities. 

Using genetic information to infer observable characteristics of an organism, such as growth temperature preferences, pH tolerance, or growth rate. This helps understand how organisms behave without culturing them. 

Individual genome sequences reconstructed from metagenomic data through binning. These represent the complete genetic blueprints of organisms in your sample, even if they’ve never been cultured in a laboratory. 

Identifying disease-causing organisms in your sample through genetic signatures. This provides rapid assessment of health risks without needing to culture organisms.